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BMRB: 15710

2K2M

Structural Basis of PxxDY Motif Recognition in SH3 Binding

Authors

Aitio, O., Hellman, M., Kesti, T., Kleino, I., Samuilova, O., Tossavainen, H., Saksela, K., Permi, P.

Assembly

Eps8L1SH3

Entity

1. Eps8L1SH3 (polymer, Thiol state: all free), 68 monomers, 7627.475 Da Detail

GPLGSGALKW VLCNYDFQAR NSSELSVKQR DVLEVLDDSR KWWKVRDPAG QEGYVPYNIL TPYPAAAS

Formula weight

7627.475 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 86.6 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.6 % (687 of 793)	92.3 % (381 of 413)	78.9 % (243 of 308)	87.5 % (63 of 72)
Backbone	80.9 % (322 of 398)	93.4 % (127 of 136)	67.8 % (135 of 199)	95.2 % (60 of 63)
Sidechain	93.2 % (427 of 458)	91.7 % (254 of 277)	98.8 % (170 of 172)	33.3 % (3 of 9)
Aromatic	98.7 % (77 of 78)	100.0 % (39 of 39)	97.2 % (35 of 36)	100.0 % (3 of 3)
Methyl	98.6 % (69 of 70)	97.1 % (34 of 35)	100.0 % (35 of 35)

1. Eps8L1SH3

GPLGSGALKW VLCNYDFQAR NSSELSVKQR DVLEVLDDSR KWWKVRDPAG QEGYVPYNIL TPYPAAAS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

LACS Plot; CA

Referencing offset: -0.32 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.32 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K2M, Strand ID: A Detail

Release date

2008-08-27

Citation

Structural basis of PxxDY motif recognition in SH3 binding
Aitio, O., Hellman, M., Kesti, T., Kleino, I., Samuilova, O., Paakkonen, K., Tossavainen, H., Saksela, K., Permi, P.
J. Mol. Biol. (2008), 382, 167-178, PubMed 18644376 , DOI 10.1016/j.jmb.2008.07.008 , Abstract

Related entities 1. Eps8L1SH3, : 1 : 2 : 135 entities Detail

Interaction partners 1. Eps8L1SH3, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

3 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

4 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

5 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

6 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

7 3D iHNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

8 3D iHNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

9 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

10 3D CC(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

11 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

12 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

13 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	Eps8L1SH3	[U-13C; U-15N]		0.8 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15710_2k2m.nef
Input source #2: Coordindates	2k2m.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

-----480-------490-------500-------510-------520-------530-------540
GPLGSGALKWVLCNYDFQARNSSELSVKQRDVLEVLDDSRKWWKVRDPAGQEGYVPYNILTPYPAAAS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSGALKWVLCNYDFQARNSSELSVKQRDVLEVLDDSRKWWKVRDPAGQEGYVPYNILTPYPAAAS
--------10--------20--------30--------40--------50--------60--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	68	0	0	100.0

Content subtype: combined_15710_2k2m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	679		97.1 (chain: A, length: 68)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1365 (1)	noe	89.7 (chain: A, length: 68)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 382
  - ¹³C chemical shifts: 235
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 89.7%
- Total number of restraints: 1364
- Weight of restraints: 1.0 (1364)
- Potential type of restraints: upper-bound-parabolic (1364)
- Range of distance target values: 2.73, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords PROTEIN