SMTL ID : 4mmz.1

Integrin AlphaVBeta3 ectodomain bound to an antagonistic tenth domain of Fibronectin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-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: 5 residues within 4Å: Chain A: E.15, G.16, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: Y.450, P.451, N.458, T.460, C.472, N.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.474 NAG-NAG.4: 3 residues within 4Å: Chain A: N.821, Q.885, G.887 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: N.371, S.398, I.399, E.400 Ligands: NAG.19 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- MAN- MAN: alpha-D-mannopyranose-(1-4)-beta-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-BMA-MAN-MAN.2: 7 residues within 4Å: Chain A: A.213, Q.214, F.217, Y.254, S.263, L.264, N.266 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.213, A:F.217 Hydrogen bonds: A:Q.214, A:Q.214

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.6: 7 residues within 4Å: Chain A: D.621, D.622, P.624 Chain B: Y.531, Y.557, N.559, C.583 No protein-ligand interaction detected (PLIP)

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

NAG.7: 4 residues within 4Å: Chain A: D.257, K.259, N.260, S.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.257, A:N.260, A:S.262 NAG.8: 5 residues within 4Å: Chain A: K.501, F.558, P.583, N.585 Chain B: D.512 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.805 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.805 NAG.10: 2 residues within 4Å: Chain A: T.942, N.943 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.943 NAG.11: 4 residues within 4Å: Chain A: D.751, H.752, T.948, N.950 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain B: N.99, S.398 Ligands: NAG-NAG.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.99, B:S.101 NAG.20: 6 residues within 4Å: Chain A: R.248, M.272 Chain B: N.316, L.317, N.320, E.323 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.316 Hydrogen bonds: B:N.320, A:R.248 NAG.21: 4 residues within 4Å: Chain B: L.645, K.646, D.647, N.654 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.647, B:D.647, B:D.647

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

MN.12: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.230, A:D.234, A:I.236, A:D.238, A:D.238 MN.13: 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.14: 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.15: 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 MN.16: 4 residues within 4Å: Chain A: C.596, 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.22: 4 residues within 4Å: Chain B: D.119, S.121, E.220 Chain C: D.79 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:S.121, B:E.220, C:D.79, H2O.1, H2O.1 MN.23: 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.1 MN.24: 6 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220, H.255 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

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

NA.17: 4 residues within 4Å: Chain A: D.544, E.545, S.546, E.547 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.547

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 3 residues within 4Å: Chain A: D.148, D.150 Ligands: GOL.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.148, A:D.148, A:D.150 GOL.25: 5 residues within 4Å: Chain A: D.148 Chain C: T.75, N.81, E.82 Ligands: GOL.18 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.148, C:T.75, C:T.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Agthoven, J.F. et al., Structural basis for pure antagonism of integrin alpha V beta 3 by a high-affinity form of fibronectin. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-03-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-V

Integrin beta-3

Fibronectin

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