SMTL ID : 3ije.1

Crystal structure of the complete integrin alhaVbeta3 ectodomain plus an Alpha/beta transmembrane fragment

Coordinates

PDB Format

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: 6 residues within 4Å: Chain A: G.16, S.17, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: D.257, N.260 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: Y.450, N.458, T.460, C.472 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: F.558, E.560, P.583, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: P.819, M.820, N.821, Q.885, G.887 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: T.942, N.943 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: S.369, N.371, S.398, I.399, E.400 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-4)-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.3: 9 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, Y.265, N.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Hydrophobic interactions: A:A.213, A:F.217

2 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.8: 3 residues within 4Å: Chain A: D.751, S.919, N.950 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 5 residues within 4Å: Chain A: P.624, R.698 Chain B: Y.531, Y.557, N.559 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.624

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

NAG.11: 1 residues within 4Å: Chain A: N.524 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.804, N.805 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain B: N.99, S.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.398, B:S.398 NAG.19: 4 residues within 4Å: Chain A: R.248 Chain B: N.316, N.320, E.323 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.316 Hydrogen bonds: B:E.323 NAG.20: 2 residues within 4Å: Chain B: S.445, N.452 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.13: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.230, A:I.236, A:D.238, A:D.238 CA.14: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, A:D.292 CA.15: 6 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357, N.377 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.351, A:D.353, A:F.355, A:D.357, A:D.357 CA.16: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421, A:D.421 CA.17: 5 residues within 4Å: Chain A: C.596, D.599, V.601, K.603, E.636 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.596, A:D.599, A:V.601, A:E.636, A:E.636 CA.21: 4 residues within 4Å: Chain B: S.123, D.126, D.127, M.335 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, J.P. et al., Crystal structure of the complete integrin alphaVbeta3 ectodomain plus an alpha/beta transmembrane fragment. J.Cell Biol. (2009)

Release Date

2009-09-29

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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