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BMRB: 18706

2LY0

Solution NMR structure of the influenza A virus S31N mutant (19-49) in presence of drug M2WJ332

Authors

Wu, Y., Wang, J., DeGrado, W.

Assembly

influenza A virus S31N mutant (19-49) in presence of drug M2WJ332

Entity

1. influenza A virus S31N mutant (19-49) in presence of drug M2WJ332, entity 1 (polymer, Thiol state: not present), 31 monomers, 3494.089 × 4 Da Detail

SNDSSDPLVV AANIIGILHL ILWILDRLFF K

2. (3S,5S,7S)-N-{[5-(thiophen-2-yl)-1,2-oxazol-3-yl]methyl}tricyclo[3.3.1.1~3,7~]decan-1-aminium (non-polymer, Thiol state: not present), 315.453 Da

Total weight

14291.81 Da

Max. entity weight

3494.089 Da

Source organism

Influenza A virus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.0 %, Completeness (bb): 83.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.0 % (329 of 378)	92.7 % (178 of 192)	78.4 % (120 of 153)	93.9 % (31 of 33)
Backbone	83.7 % (154 of 184)	95.2 % (59 of 62)	70.7 % (65 of 92)	100.0 % (30 of 30)
Sidechain	91.5 % (205 of 224)	91.5 % (119 of 130)	93.4 % (85 of 91)	33.3 % (1 of 3)
Aromatic	80.6 % (29 of 36)	94.4 % (17 of 18)	64.7 % (11 of 17)	100.0 % (1 of 1)
Methyl	100.0 % (56 of 56)	100.0 % (28 of 28)	100.0 % (28 of 28)

1. entity 1

SNDSSDPLVV AANIIGILHL ILWILDRLFF K

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	S31N	[U-100% 15N]		2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	S31N	[U-100% 13C; U-100% 15N]		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	S31N	[U-100% 13C; U-100% 15N; U-80% 2H]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
10	S31N	[U-10% 13C; U-100% 15N]		2 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
13	S31N	mixature of 50% 13C15N and 50% 12C14N		2 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
16	entity_1	13C15N of V27A30N31I33G34		2 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LY0, Strand ID: A, B, C, D Detail

Release date

2013-01-06

Citation

Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus
Wang, J., Wu, Y., Ma, C., Fiorin, G., Wang, J., Pinto, L.H., Lamb, R.A., Klein, M.L., Degrado, W.F.
Proc. Natl. Acad. Sci. U. S. A. (2013), 110, 1315-1320, PubMed 23302696 , DOI 10.1073/pnas.1216526110 , Abstract

Related entities 1. influenza A virus S31N mutant (19-49) in presence of drug M2WJ332, entity 1, : 1 : 3 : 2 : 4 : 113 entities Detail

Interaction partners 1. influenza A virus S31N mutant (19-49) in presence of drug M2WJ332, entity 1, : 12 interactors Detail

More details for 12 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	S31N	[U-100% 15N]		2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	S31N	[U-100% 13C; U-100% 15N]		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	S31N	[U-100% 13C; U-100% 15N; U-80% 2H]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

4 3D HN(CA)CB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	S31N	[U-100% 13C; U-100% 15N; U-80% 2H]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	S31N	[U-100% 13C; U-100% 15N; U-80% 2H]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	S31N	[U-100% 13C; U-100% 15N]		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
13	S31N	mixature of 50% 13C15N and 50% 12C14N		2 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
16	entity_1	13C15N of V27A30N31I33G34		2 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
10	S31N	[U-10% 13C; U-100% 15N]		2 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

10 3D CCH_TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	S31N	[U-100% 13C; U-100% 15N]		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18706_2ly0.nef
Input source #2: Coordindates	2ly0.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	None
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)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
E	1	A2Y	(3S,5S,7S)-N-{[5-(thiophen-2-yl)-1,2-oxazol-3-yl]methyl}tricyclo[3.3.1.1~3,7~]decan-1-aminium	None

Sequence alignments

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

-20-------30--------40---------
SNDSSDPLVVAANIIGILHLILWILDRLFFK
|||||||||||||||||||||||||||||||
SNDSSDPLVVAANIIGILHLILWILDRLFFK
--------10--------20--------30-

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

-20-------30--------40---------
SNDSSDPLVVAANIIGILHLILWILDRLFFK
|||||||||||||||||||||||||||||||
SNDSSDPLVVAANIIGILHLILWILDRLFFK
--------10--------20--------30-

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

-20-------30--------40---------
SNDSSDPLVVAANIIGILHLILWILDRLFFK
|||||||||||||||||||||||||||||||
SNDSSDPLVVAANIIGILHLILWILDRLFFK
--------10--------20--------30-

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

-20-------30--------40---------
SNDSSDPLVVAANIIGILHLILWILDRLFFK
|||||||||||||||||||||||||||||||
SNDSSDPLVVAANIIGILHLILWILDRLFFK
--------10--------20--------30-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	31	0	0	100.0
B	B	31	0	0	100.0
C	C	31	0	0	100.0
D	D	31	0	0	100.0

Content subtype: combined_18706_2ly0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	321		96.8 (chain: A, length: 31)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1024 (1)	noe	87.1 (chain: A, length: 31), 87.1 (chain: B, length: 31), 87.1 (chain: C, length: 31), 87.1 (chain: D, length: 31)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	136 (1)	hbond	67.7 (chain: A, length: 31), 67.7 (chain: B, length: 31), 67.7 (chain: C, length: 31), 67.7 (chain: D, length: 31)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	212 (212)	.	96.8 (chain: A, length: 31), 96.8 (chain: B, length: 31), 96.8 (chain: C, length: 31), 96.8 (chain: D, length: 31)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 177
  - ¹³C chemical shifts: 114
  - ¹⁵N chemical shifts: 30
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 87.1%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 87.1%
  - Entity_assembly_ID: C, Chain length: 31, Sequence coverage: 87.1%
  - Entity_assembly_ID: D, Chain length: 31, Sequence coverage: 87.1%
- Total number of restraints: 1016
- Weight of restraints: 1.0 (1016)
- Potential type of restraints: square-well-parabolic (1016)
- Range of distance target values: 2.65, 3.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 67.7%
    - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 67.7%
    - Entity_assembly_ID: C, Chain length: 31, Sequence coverage: 67.7%
    - Entity_assembly_ID: D, Chain length: 31, Sequence coverage: 67.7%
  - Total number of restraints: 136
  - Weight of restraints: 1.0 (136)
  - Potential type of restraints: square-well-parabolic (136)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
    - Chain_ID: E
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 96.8%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 96.8%
  - Entity_assembly_ID: C, Chain length: 31, Sequence coverage: 96.8%
  - Entity_assembly_ID: D, Chain length: 31, Sequence coverage: 96.8%
- Total number of restraints: 212
- Total number of restraints per polymer type: 212
- Weight of restraints: 1.0 (212)
- Potential type of restraints: square-well-parabolic (212)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D

Keywords influenza A virus, M2 channel, S31N inhibitor