SMTL ID : 4g1m.1

Re-refinement of alpha V beta 3 structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 7 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 4 residues within 4Å: Chain A: D.257, K.259, N.260, S.262 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: P.451, N.458, T.460, C.472 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.460 NAG-NAG.5: 3 residues within 4Å: Chain A: Q.494, S.522, N.524 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: F.558, E.560, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: P.819, N.821, Q.885, G.887 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: T.942, N.943 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: D.751, I.869, S.919, N.950 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: R.248 Chain B: N.316, L.317, N.320 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: N.371, S.398, I.399, E.400 Ligands: NAG.23 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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-MAN-MAN-MAN.3: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, N.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214, A:Q.214, A:Q.214 Hydrophobic interactions: A:A.213, A:F.217

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.12: 5 residues within 4Å: Chain A: P.624 Chain B: Y.531, Y.557, N.559, C.583 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.624

7 x CA: CALCIUM ION(Non-covalent)

CA.13: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.230, A:I.236, A:D.238, A:D.238, H2O.1 CA.14: 6 residues within 4Å: Chain A: D.284, I.285, N.286, D.288, Y.290, D.292 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, H2O.1 CA.15: 5 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:D.353, A:F.355, A:D.357 CA.16: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421, H2O.1 CA.17: 5 residues within 4Å: Chain A: C.596, G.597, D.599, V.601, E.636 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.596, A:D.599, A:V.601, A:E.636, H2O.1 CA.21: 6 residues within 4Å: Chain B: D.119, S.121, S.123, E.220, D.251, A.252 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.121, B:S.123, B:D.251 CA.22: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335, H2O.3

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

NAG.18: 1 residues within 4Å: Chain A: N.674 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain A: N.804, N.805 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.804 NAG.23: 3 residues within 4Å: Chain B: N.99 Ligands: NAG-NAG.11, NAG-NAG.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99 NAG.24: 2 residues within 4Å: Chain B: N.450, N.452 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.20: 4 residues within 4Å: Chain A: S.705, E.706, M.707, D.708 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.707

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, X. et al., Alpha V Beta 3 Integrin Crystal Structures and their Functional Implications. Biochemistry (2012)

Release Date

2012-12-12

Peptides

Integrin alpha-V: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-V

Integrin beta-3

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