SMTL ID : 4wk2.1

Metal Ion and Ligand Binding of Integrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

GLY-ARG-GLY-ASP-SER-PRO.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 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.133, A:F.187 Hydrogen bonds: B:Y.133, B:S.134, B:N.224, B:N.224, B:N.224, B:L.225, A:Y.186, A:Q.189, A:Q.221 Water bridges: B:S.227, B:E.229 Salt bridges: A:D.227

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.2: 13 residues within 4Å: Chain A: R.220, Q.221, A.222, S.223, Y.226, L.231, Y.261, T.263, S.272, L.273, Y.274, N.275 Ligands: NAG-NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.222, A:Y.226 Hydrogen bonds: 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: 6 residues within 4Å: Chain A: N.256, Y.259, Y.261, N.275, S.277 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: S.241, D.243, N.266, S.268, D.269, L.273 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: W.247, R.248, N.249, R.252, T.431 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: Y.380, G.384, N.386 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.4: 9 residues within 4Å: Chain A: P.14, P.15, G.16, S.17, K.41, A.42, N.43, L.50, Q.51 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.8: 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:T.245, A:D.247, A:D.247 CA.9: 6 residues within 4Å: Chain A: D.293, V.294, N.295, D.297, L.299, D.301 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.10: 6 residues within 4Å: Chain A: D.360, L.361, D.362, D.364, Y.366, D.368 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.362, A:D.364, A:Y.366, A:D.368, H2O.1 CA.11: 7 residues within 4Å: Chain A: D.424, L.425, D.426, N.428, Y.430, D.432, G.448 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.424, A:D.426, A:Y.430, A:D.432, A:D.432 CA.14: 4 residues within 4Å: Chain B: S.134, M.135, D.137, D.138 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.134, B:D.137, B:D.138, H2O.4, H2O.7 CA.15: 6 residues within 4Å: Chain B: E.169, N.224, D.226, P.228, E.229, H.263 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.12: 5 residues within 4Å: Chain A: P.28, G.29, G.32, N.141, F.142 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.28 Hydrogen bonds: A:N.141 NAG.16: 3 residues within 4Å: Chain B: K.382, N.383, N.397 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.382, B:N.383, B:N.397 NAG.17: 5 residues within 4Å: Chain B: D.137, E.140, N.141, A.342, N.343 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.140 Hydrogen bonds: B:N.343 Water bridges: B:N.141 NAG.18: 2 residues within 4Å: Chain B: N.192, R.220 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 6 residues within 4Å: Chain B: S.132, Y.133, S.134, N.224, E.229 Ligands: GLY-ARG-GLY-ASP-SER-PRO.1 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.132, B:S.134, B:E.229, H2O.4, H2O.4

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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