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BMRB: 19305

2M9P

NMR structure of an inhibitor bound dengue NS3 protease

Authors

Gibbs, A., Tounge, B., Steele, R.

Assembly

an inhibitor bound dengue NS3 protease

Entity

1. an inhibitor bound dengue NS3 protease, entity 1 (polymer, Thiol state: not present), 240 monomers, 25315.00 Da Detail

GSAADLELER AADVKWEDQA EISGSSPILS ITISEDGSMS IKNEEEEQTL GGGGSGGGGE FAGVLWDVPS PPPVGKAELE DGAYRIKQKG ILGYSQIGAG VYKEGTFHTM WHVTRGAVLM HKGKRIEPSW ADVKKDLISY GGGWKLEGEW KEGEEVQVLA LEPGKNPRAV QTKPGLFKTN AGTIGAVSLD FSPGTSGSPI IDKKGKVVGL YGNGVVTRSG AYVSAIAQTE KSIEDNPEIE

2. ketobenzene (polymer, Thiol state: not present), 5 monomers, 730.8440 Da Detail

XXKRX

Total weight

26045.844 Da

Max. entity weight

25315.0 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.1 %, Completeness: 56.0 %, Completeness (bb): 78.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	56.0 % (1504 of 2685)	36.9 % (515 of 1395)	73.5 % (766 of 1042)	89.9 % (223 of 248)
Backbone	78.9 % (1127 of 1428)	53.6 % (273 of 509)	93.0 % (641 of 689)	92.6 % (213 of 230)
Sidechain	38.5 % (563 of 1462)	27.2 % (241 of 886)	56.1 % (313 of 558)	50.0 % (9 of 18)
Aromatic	18.6 % (32 of 172)	19.8 % (17 of 86)	11.2 % (9 of 80)	100.0 % (6 of 6)
Methyl	73.2 % (183 of 250)	66.4 % (83 of 125)	80.0 % (100 of 125)

1. entity 1

GSAADLELER AADVKWEDQA EISGSSPILS ITISEDGSMS IKNEEEEQTL GGGGSGGGGE FAGVLWDVPS PPPVGKAELE DGAYRIKQKG ILGYSQIGAG VYKEGTFHTM WHVTRGAVLM HKGKRIEPSW ADVKKDLISY GGGWKLEGEW KEGEEVQVLA LEPGKNPRAV QTKPGLFKTN AGTIGAVSLD FSPGTSGSPI IDKKGKVVGL YGNGVVTRSG AYVSAIAQTE KSIEDNPEIE

2. ketobenzene

XXKRX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2M9P, Strand ID: A Detail

Release date

2014-07-06

Citation

NMR structure of an inhibitor bound dengue NS3 protease provides new insights into the NS2B NS3 ligand interactions
Gibbs, A., Tounge, B., Steele, R.
Not known

Related entities 1. an inhibitor bound dengue NS3 protease, entity 1, : 37 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

2 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

9 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

10 3D CCH-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

11 3D CNH-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

12 3D NCH-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		0.8 mM
2	entity_1	[U-5% 13C; U-100% 15N]		0.8 mM
3	entity_1	[U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM		0.8 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19305_2m9p.nef
Input source #2: Coordindates	2m9p.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:1:BEZ:C	2:2:NLE:N	unknown	unknown	n/a
2:2:NLE:C	2:3:LYS:N	unknown	unknown	n/a
2:4:ARG:C	2:5:M9P:N	unknown	unknown	n/a
1:196:SER:OG	2:5:M9P:CI	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	251	BEZ	BENZOIC ACID	Assigned chemical shifts, Coordinates
B	252	NLE	NORLEUCINE	Assigned chemical shifts, Coordinates
B	255	M9P	amino{[(4S,5S)-4-amino-6,6,6-trifluoro-5-hydroxyhexyl]amino}methaniminium	Assigned chemical shifts, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI

-------210-------220-------230-------240
IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE
||||||||||||||||||||||||||||||||||||||||
IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-----
XXKRX
|||||
XXKRX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	240	0	0	100.0
B	B	5	0	0	100.0

Content subtype: combined_19305_2m9p.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1298		93.8 (chain: A, length: 240), 100.0 (chain: B, length: 5)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1630 (1)	noe	87.9 (chain: A, length: 240)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	240 (1)	noe	56.2 (chain: A, length: 240)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	130 (1)	hbond	29.6 (chain: A, length: 240)
4	Distance restraints	CNS/XPLOR_distance_constraints_7	Warning	130 (1)	hbond	29.6 (chain: A, length: 240)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	287 (287)	.	80.4 (chain: A, length: 240)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 240, Sequence coverage: 93.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG
 |||||||||||||||||||||||||||||||||||||||||   ||||||  |||  ||||||||||||  ||||| | ||||||||||||||||||||
.SAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIK...EEQTLG..GSG..GEFAGVLWDVPS..PVGKA.L.DGAYRIKQKGILGYSQIGAG

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI
||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
VYKEGTFHTMWHVTRGAVLMHKGKRIE.SWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFS.GTSGSPI

-------210-------220-------230-------240
IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE
||||||||||||||||| ||||||||||||||||||||||
IDKKGKVVGLYGNGVVT.SGAYVSAIAQTEKSIEDNPEIE

Entity_assembly_ID: B, Chain length: 5, Sequence coverage: 100.0%

-----
XXKRX
|||||
XXKRX

Total number of assignments
- ¹³C chemical shifts: 712
- ¹H chemical shifts: 369
- ¹⁵N chemical shifts: 217

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
23	SER	HG	6.173
25	SER	HG	6.169
34	SER	HG	6.167
40	SER	HG	6.06
109	THR	HG1	6.637
114	THR	HG1	4.888
129	SER	HG	4.287
172	THR	HG1	6.174
179	THR	HG1	6.114
192	SER	HG	6.327
195	THR	HG1	6.324
198	SER	HG	5.972
217	THR	HG1	5.127
224	SER	HG	5.289
229	THR	HG1	6.343
232	SER	HG	6.117

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1031	712	69.1
¹H chemical shifts	1376	310	22.5
¹⁵N chemical shifts	252	217	86.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	480	438	91.2
¹H chemical shifts	505	210	41.6
¹⁵N chemical shifts	228	208	91.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	551	274	49.7
¹H chemical shifts	871	100	11.5
¹⁵N chemical shifts	24	9	37.5

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	128	101	78.9
¹H chemical shifts	128	84	65.6

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	80	0	0.0
¹H chemical shifts	86	6	7.0
¹⁵N chemical shifts	6	6	100.0

Entity_assemble_ID: B

Peptide bond of PRO
Rotameric state of ILE , LEU, and VAL
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: A
- Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 240, Sequence coverage: 87.9%
- Total number of restraints: 1630
- Weight of restraints: 1.0 (1630)
- Potential type of restraints: square-well-parabolic (1630)
- Range of distance target values: 2.25, 4.15 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 240, Sequence coverage: 56.2%
  - Total number of restraints: 240
  - Weight of restraints: 1.0 (240)
  - Potential type of restraints: square-well-parabolic (240)
  - Range of distance target values: 2.73, 4.75 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 240, Sequence coverage: 29.6%
    - Total number of restraints: 130
    - Weight of restraints: 1.0 (130)
    - Potential type of restraints: square-well-parabolic (130)
    - Range of distance target values: 1.9, 2.55 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_7
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 240, Sequence coverage: 29.6%
      - Total number of restraints: 130
        Total hydrogen bond restraints: 130
        O...H-x: 15
        O...h-N (too close!): 15
        Long range: 100
        O...H-x: 50
        O...h-N (too close!): 49
        O...h-N: 1
      - Weight of restraints: 1.0 (130)
        Total hydrogen bond restraints: 1.0 (130)
        O...H-x: 1.0 (15)
        O...h-N (too close!): 1.0 (15)
        Long range: 1.0 (100)
        O...H-x: 1.0 (50)
        O...h-N (too close!): 1.0 (49)
        O...h-N: 1.0 (1)
      - Potential type of restraints: square-well-parabolic (130)
        Total hydrogen bond restraints: square-well-parabolic (130)
        O...H-x: square-well-parabolic (15)
        O...h-N (too close!): square-well-parabolic (15)
        Long range: square-well-parabolic (100)
        O...H-x: square-well-parabolic (50)
        O...h-N (too close!): square-well-parabolic (49)
        O...h-N: square-well-parabolic (1)
      - Range of distance target values: 1.85, 2.62 (Å)
      - Histogram of distance target values
      - Histogram of discrepancy in distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 240, Sequence coverage: 80.4%
- Total number of restraints: 287
- Total number of restraints per polymer type: 287
- Weight of restraints: 1.0 (287)
- Potential type of restraints: square-well-parabolic (287)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords covalent ligand, NS2B cofactor, NS3 protease