SMTL ID : 1m1x.1

CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN ALPHA VBETA3 BOUND TO MN2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 7 residues within 4Å: Chain A: E.15, G.16, K.42, N.44, V.51, E.52, H.91 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 3 residues within 4Å: Chain A: F.558, E.560, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: D.751, 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.4: 2 residues within 4Å: Chain A: T.942, N.943 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.742, A:N.943 NAG-NDG.6: 5 residues within 4Å: Chain A: D.622, P.624, I.654 Chain B: Y.557, N.559 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.559 Hydrophobic interactions: A:I.654 NAG-NDG.7: 9 residues within 4Å: Chain B: K.646, D.647, T.648, G.649, K.650, A.652, N.654, R.666, Q.668 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.649 Hydrophobic interactions: B:K.646

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

NAG.8: 2 residues within 4Å: Chain A: D.257, N.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.257 NAG.9: 8 residues within 4Å: Chain A: P.451, I.453, L.454, N.455, N.458, T.460, S.471, C.472 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.451 Hydrogen bonds: A:N.455, A:N.458, A:C.472 NAG.15: 4 residues within 4Å: Chain A: R.248 Chain B: N.316, L.317, N.320 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.316 Hydrogen bonds: B:N.316, B:N.320, A:R.248, A:R.248 NAG.16: 2 residues within 4Å: Chain B: N.371, E.400 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.371, B:S.398, B:S.398

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

MN.10: 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:N.232, A:I.236, A:D.238 MN.11: 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 MN.12: 6 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, N.356, D.357 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.351, A:D.353, A:F.355, A:D.357 MN.13: 6 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, P.420, D.421 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:P.420, A:D.421 MN.14: 5 residues within 4Å: Chain A: C.596, G.597, D.599, V.601, E.636 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.599, A:D.599, A:V.601, A:E.636, A:E.636 MN.17: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.123, B:D.126, 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 extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand. Science (2002)

Release Date

2002-08-14

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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