BMRBj - BMREntryMaster

Found 1 Document (1.035 seconds)

BMRB: 19906

2MNU

Backbone and side chain 1H, 13C, and 15N Chemical Shift Assignments for EDB and specific binding aptide

Authors

Suh, J., Yu, T.

Assembly

EDB and specific binding aptide

Entity

1. EDB (polymer, Thiol state: not present), 93 monomers, 9857.817 Da Detail

GSEVPQLTDL SFVDITDSSI GLRWTPLNSS TIIGYRITVV AAGEGIPIFE DFVDSSVGYY TVTGLEPGID YDISVITLIN GGESAPTTLT QQT

2. APT (polymer, Thiol state: not present), 26 monomers, 3075.390 Da Detail

SSSPIQGSWT WENGKWTWKG IIRLEQ

Total weight

12933.207 Da

Max. entity weight

9857.817 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 74.7 %, Completeness (bb): 79.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.7 % (1000 of 1338)	80.6 % (548 of 680)	65.0 % (346 of 532)	84.1 % (106 of 126)
Backbone	79.1 % (555 of 702)	91.0 % (223 of 245)	66.9 % (230 of 344)	90.3 % (102 of 113)
Sidechain	74.0 % (549 of 742)	74.7 % (325 of 435)	74.8 % (220 of 294)	30.8 % (4 of 13)
Aromatic	38.5 % (47 of 122)	49.2 % (30 of 61)	26.8 % (15 of 56)	40.0 % (2 of 5)
Methyl	78.6 % (121 of 154)	84.4 % (65 of 77)	72.7 % (56 of 77)

1. EDB

GSEVPQLTDL SFVDITDSSI GLRWTPLNSS TIIGYRITVV AAGEGIPIFE DFVDSSVGYY TVTGLEPGID YDISVITLIN GGESAPTTLT QQT

2. APT

SSSPIQGSWT WENGKWTWKG IIRLEQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6

#	Name	Isotope labeling	Concentration
1	EDB	[U-100% 13C; U-100% 15N]	0.3 mM
2	APT	[U-100% 13C; U-100% 15N]	0.3 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MNU, Strand ID: A, B Detail

Release date

2014-09-21

Citation

An unusual protein-protein interaction through coupled unfolding and binding
Yu, T., Shin, S., Kim, E., Kim, S., Ryu, K., Cheong, H., Ahn, H., Jon, S., Suh, J.
Angew. Chem Int Ed Engl. (2014), 53, 9784-9787, PubMed 24985319 , DOI 10.1002/anie.201404750 , Abstract

Related entities 1. EDB, : 6 : 346 entities Detail

Related entities 2. APT, : 1 : 1 entities Detail

Interaction partners 1. EDB, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 5 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19906_2mnu.nef
Input source #2: Coordindates	2mnu.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

None

Sequence alignments

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

------10--------20--------30--------40--------50--------60--------70--------80--------90-----
GSEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQT
--------10--------20--------30--------40--------50--------60--------70--------80--------90---

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

-------210-------220------
SSSPIQGSWTWENGKWTWKGIIRLEQ
||||||||||||||||||||||||||
SSSPIQGSWTWENGKWTWKGIIRLEQ
--------10--------20------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0
B	B	26	0	0	100.0

Content subtype: combined_19906_2mnu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	981		95.7 (chain: A, length: 93), 100.0 (chain: B, length: 26)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1887 (1)	noe	95.7 (chain: A, length: 93), 96.2 (chain: B, length: 26)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	107 (1)	noe	11.8 (chain: A, length: 93), 57.7 (chain: B, length: 26)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	hbond	15.4 (chain: B, length: 26)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	225 (225)	.	98.9 (chain: A, length: 93), 100.0 (chain: B, length: 26)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	72 (72)	.	53.8 (chain: A, length: 93), 84.6 (chain: B, length: 26)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 95.7%
  - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 549
  - ¹³C chemical shifts: 328
  - ¹⁵N chemical shifts: 104
- Completeness of assignments
  - Entity_assemble_ID: A
  - 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
25	ARG	HH21	6.6
25	ARG	HH22	6.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	509	393	77.2
¹³C chemical shifts	409	242	59.2
¹⁵N chemical shifts	96	76	79.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	191	173	90.6
¹³C chemical shifts	186	89	47.8
¹⁵N chemical shifts	88	76	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	318	220	69.2
¹³C chemical shifts	223	153	68.6
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	57	85.1
¹³C chemical shifts	67	45	67.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	37	11	29.7
¹³C chemical shifts	36	5	13.9
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	171	154	90.1
¹³C chemical shifts	123	86	69.9
¹⁵N chemical shifts	33	28	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	53	98.1
¹³C chemical shifts	52	26	50.0
¹⁵N chemical shifts	25	24	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	101	86.3
¹³C chemical shifts	71	60	84.5
¹⁵N chemical shifts	8	4	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	9	90.0
¹³C chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	19	79.2
¹³C chemical shifts	20	10	50.0
¹⁵N chemical shifts	4	2	50.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 95.7%
  - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 96.2%
- Total number of restraints: 1880
- Weight of restraints: 1.0 (1880)
- Potential type of restraints: square-well-parabolic (1880)
- Range of distance target values: 2.23, 4.19 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 11.8%
    - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 57.7%
  - Total number of restraints: 107
  - Weight of restraints: 1.0 (107)
  - Potential type of restraints: square-well-parabolic (107)
  - Range of distance target values: 2.45, 4.15 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 15.4%
    - Total number of restraints: 4
    - Weight of restraints: 1.0 (4)
    - Potential type of restraints: square-well-parabolic (4)
    - Range of distance target values: 2.15, 2.15 (Å)
    - Distance restraints per residue
      - Chain_ID: A
        None
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 98.9%
  - Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 100.0%
- Total number of restraints: 225
- Total number of restraints per polymer type: 225
- Weight of restraints: 1.0 (225)
- Potential type of restraints: square-well-parabolic (225)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 53.8%

------10--------20--------30--------40--------50--------60--------70--------80--------90-----
GSEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQT
         |||||| ||||||||  ||| | |   || ||| |      |||||||||||| ||| || ||||||||               
.........LSFVDI.DSSIGLRW..LNS.T.I...IT.VAA.E......DFVDSSVGYYTV.GLE.GI.YDISVITL               
------10--------20--------30--------40--------50--------60--------70--------80

Entity_assembly_ID: B, Chain length: 26, Sequence coverage: 84.6%

-------210-------220------
SSSPIQGSWTWENGKWTWKGIIRLEQ
  | |||||||| |||||||||||||
..S.IQGSWTWE.GKWTWKGIIRLEQ

Total number of restraints: 72
Potential type of restraints: undefined (72)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords EDB, aptide

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Found 1 Document (1.035 seconds)

BMRB: 19906

Sample

Related entities 1. EDB, : 6 : 346 entities Detail

Related entities 2. APT, : 1 : 1 entities Detail

Interaction partners 1. EDB, : 1 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail