SMTL ID : 1l5g.1

CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN AVB3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- GLY- ASP- PHE- MVA: CYCLIC ARG-GLY-ASP PEPTIDE(Non-covalent)

ARG-GLY-ASP-PHE-MVA.1: 14 residues within 4Å: Chain A: D.150, Y.178, Q.180, D.218 Chain B: S.121, Y.122, S.123, R.214, N.215, R.216, D.217, A.218, E.220 Ligands: MN.18 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.122, A:Y.178 Hydrogen bonds: B:Y.122, B:N.215, B:R.216, A:D.150, A:Y.178 Salt bridges: A:D.218

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.2: 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) NAG-NAG.3: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, N.266 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.213, A:F.217 Hydrogen bonds: A:Q.214 NAG-NAG.4: 3 residues within 4Å: Chain A: F.558, E.560, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: D.751, H.870, T.948, N.950 No protein-ligand interaction detected (PLIP)

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

NAG-NDG.5: 2 residues within 4Å: Chain A: T.942, N.943 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.943 NAG-NDG.7: 5 residues within 4Å: Chain A: D.621, D.622, I.654 Chain B: Y.557, N.559 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.654, A:I.654 Hydrogen bonds: A:D.621 NAG-NDG.8: 10 residues within 4Å: Chain A: N.759 Chain B: K.646, D.647, T.648, G.649, K.650, A.652, N.654, R.666, Q.668 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.652, B:R.666

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

NAG.9: 3 residues within 4Å: Chain A: D.257, N.260, S.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.257, A:N.260, A:S.262, A:S.262 NAG.10: 7 residues within 4Å: Chain A: I.453, L.454, N.455, N.458, T.460, S.471, C.472 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.453, A:N.455, A:N.458, A:T.460, A:T.460, A:S.471 NAG.16: 3 residues within 4Å: Chain A: M.272 Chain B: N.316, N.320 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.316 Hydrogen bonds: B:N.320 NAG.17: 2 residues within 4Å: Chain B: N.371, S.398 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.371, B:S.398, B:S.398

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.11: 7 residues within 4Å: Chain A: D.230, N.232, D.234, G.235, I.236, D.237, D.238 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.230, A:I.236, A:D.238 MN.12: 6 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292, Q.320 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 MN.13: 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 MN.14: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421 MN.15: 6 residues within 4Å: Chain A: C.596, D.599, N.600, V.601, C.602, 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 MN.18: 5 residues within 4Å: Chain B: D.119, S.121, S.123, E.220 Ligands: ARG-GLY-ASP-PHE-MVA.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.121, B:S.123, B:E.220 MN.19: 4 residues within 4Å: Chain B: S.123, D.126, D.127, D.251 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.251, B:D.251 MN.20: 5 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.158, B:D.217, B:P.219, B:E.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, J.P. et al., Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand. Science (2002)

Release Date

2002-04-17

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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