SMTL ID : 3fcs.1 (1 other biounit)

Structure of complete ectodomain of integrin aIIBb3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

2 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: 2 residues within 4Å: Chain B: N.99 Ligands: NAG-NAG-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.449, N.450, G.451, N.452 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN.2: 7 residues within 4Å: Chain A: W.262, R.281, M.285 Chain B: N.316, L.317, N.320, K.600 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.281

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN.3: 6 residues within 4Å: Chain B: S.369, N.371, P.381, S.398, E.400 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-MAN.5: 7 residues within 4Å: Chain A: D.628, V.630, M.660 Chain B: Y.531, Y.557, N.559, C.583 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, T.251, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.243, A:D.245, A:D.247, A:T.250, A:T.250 CA.7: 5 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.297, A:D.301, A:R.303, A:D.305, H2O.1 CA.8: 5 residues within 4Å: Chain A: D.365, D.367, D.369, Y.371, D.373 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.365, A:D.367, A:D.369, A:Y.371, A:D.373 CA.9: 5 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.426, A:D.428, A:Y.432, A:D.434, A:D.434 CA.10: 4 residues within 4Å: Chain A: C.602, D.605, V.607, E.642 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.602, A:D.605, A:V.607, A:E.642, H2O.4 CA.15: 4 residues within 4Å: Chain B: S.123, 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.10 CA.16: 5 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.158, B:D.217, B:D.217, B:P.219, B:E.220

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

NAG.11: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG.12: 6 residues within 4Å: Chain A: N.505, E.507, R.512, N.570, V.571, S.572 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.505, A:E.507 Hydrogen bonds: A:E.507, A:R.512

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.13: 5 residues within 4Å: Chain A: Q.463, N.467, S.483, C.484, F.485 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.463, A:N.467, A:C.484

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 4 residues within 4Å: Chain B: D.119, S.121, E.220, D.251 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.121, H2O.9, H2O.12, H2O.12, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J. et al., Structure of a complete integrin ectodomain in a physiologic resting state and activation and deactivation by applied forces. Mol.Cell (2008)

Release Date

2009-01-20

Peptides

Integrin, alpha 2b: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin, alpha 2b

Integrin beta-3

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