SMTL ID : 4wjk.1

Metal Ion and Ligand Binding of Integrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 11 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 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.223, A:S.223, A:Y.226 Hydrophobic interactions: A:A.222, A:Y.226

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.256, L.257, Y.259, S.277, E.279 Chain B: E.327 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.327

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.3: 9 residues within 4Å: Chain A: P.14, P.15, G.16, S.17, K.41, A.42, N.43, L.50, Q.51 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.50

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

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: 3 residues within 4Å: Chain B: E.89, N.249, 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)

1 x NAG- NAG- BMA- MAN: 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.7: 3 residues within 4Å: Chain B: K.382, N.383, N.397 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:D.243, A:T.245, A:D.247 CA.9: 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.2 CA.10: 7 residues within 4Å: Chain A: D.360, L.361, D.362, D.364, Y.366, D.368, G.389 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.2 CA.11: 8 residues within 4Å: Chain A: D.424, L.425, D.426, G.427, 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.13: 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.15, H2O.16 CA.14: 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain B: S.132, N.224, E.229, A.260 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.132, B:E.229, H2O.14, H2O.16, H2O.16, H2O.16

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

NAG.15: 5 residues within 4Å: Chain B: N.141, S.341, A.342, N.343, S.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.141, B:N.343

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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