SMTL ID : 4wk0.1

Metal Ion and Ligand Binding of Integrin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- GLY- ASP: ARG-GLY-ASP(Non-covalent)

ARG-GLY-ASP.1: 16 residues within 4Å: Chain A: Y.186, F.187, Q.189, Q.221, S.224, D.227 Chain B: S.132, Y.133, S.134, G.223, N.224, L.225, D.226, S.227, E.229 Ligands: MG.13 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.187 Hydrogen bonds: A:Y.186, A:Q.189, A:Q.221, B:Y.133, B:N.224, B:N.224, B:N.224, B:L.225 Water bridges: A:D.228, B:S.227, B:E.229 Salt bridges: A:D.227

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 12 residues within 4Å: Chain A: R.220, Q.221, A.222, S.223, Y.226, Y.261, T.263, S.272, L.273, Y.274, N.275 Ligands: NAG.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.222, A:Y.226 Hydrogen bonds: A:Y.226 Water bridges: A:Y.226

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 8 residues within 4Å: Chain A: P.15, G.16, S.17, K.41, A.42, N.43, L.50, Q.51 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: S.241, N.266, S.268, D.269, L.273 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: W.247, R.248, N.249, R.252, T.431 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: Y.380, G.384, V.385, N.386 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: E.239, F.240, S.241, D.243, T.245, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.239, A:S.241, A:D.243, A:T.245, A:D.247 CA.8: 7 residues within 4Å: Chain A: D.293, V.294, N.295, D.297, L.299, D.301, L.328 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.293, A:D.297, A:L.299, A:D.301, H2O.1 CA.9: 6 residues within 4Å: Chain A: D.360, L.361, D.362, D.364, Y.366, D.368 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.360, A:D.362, A:D.364, A:Y.366, A:D.368 CA.10: 7 residues within 4Å: Chain A: D.424, L.425, D.426, N.428, Y.430, D.432, G.448 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.424, A:D.426, A:Y.430, A:D.432, H2O.2 CA.14: 6 residues within 4Å: Chain B: S.134, M.135, D.137, D.138, A.342, N.343 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.134, B:D.138, B:A.342, H2O.16, H2O.17 CA.15: 5 residues within 4Å: Chain B: E.169, N.224, D.226, P.228, E.229 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.169, B:D.226, B:D.226, B:P.228, B:E.229

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 6 residues within 4Å: Chain A: N.256, Y.259, Y.261, N.275, S.277 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.256, A:S.277 NAG.12: 3 residues within 4Å: Chain A: P.28, N.141, F.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.141 NAG.16: 3 residues within 4Å: Chain B: K.382, N.383, N.397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.382, B:N.397 NAG.17: 3 residues within 4Å: Chain B: N.141, N.343, S.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.141, B:N.343

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 6 residues within 4Å: Chain B: S.132, S.134, N.224, E.229, A.260 Ligands: ARG-GLY-ASP.1 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.132, B:E.229, H2O.16, H2O.17, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, W. et al., Metal ion and ligand binding of integrin alpha 5 beta 1. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-12-03

Peptides

Integrin alpha-5: A
Integrin beta-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-5

Integrin beta-1

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