SMTL ID : 6naj.1

Integrin AlphaVBeta3 ectodomain bound to Hr10 variant of the 10th domain of Fibronectin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 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: 6 residues within 4Å: Chain A: E.15, G.16, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: Y.450, N.458, T.460, C.472, N.474 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.821, Q.885, V.886, 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.18 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 9 residues within 4Å: Chain A: P.758, N.759 Chain B: E.644, L.645, D.647, G.649, A.652, N.654, Q.668 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.759, B:E.644

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: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, 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)

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

NAG.8: 4 residues within 4Å: Chain A: D.257, K.259, N.260, S.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.257, A:K.259, A:K.259, A:S.262 NAG.9: 5 residues within 4Å: Chain A: K.501, F.558, E.560, N.585 Chain B: D.512 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.558 NAG.10: 1 residues within 4Å: Chain A: N.805 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain A: T.942, N.943 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.943 NAG.12: 5 residues within 4Å: Chain A: D.751, H.752, S.919, T.948, N.950 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.751, A:S.919, A:N.950 NAG.18: 3 residues within 4Å: Chain B: K.98, N.99 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99 NAG.19: 5 residues within 4Å: Chain A: R.248, M.272 Chain B: N.316, L.317, N.320 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.248 Hydrophobic interactions: B:N.316

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

MN.13: 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:D.234, A:I.236, A:D.238 MN.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.288, A:D.288, A:Y.290, A:D.292, A:D.292 MN.15: 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.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 MN.17: 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.20: 5 residues within 4Å: Chain B: D.119, S.121, S.123, E.220 Chain C: D.79 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.79, B:S.121, B:E.220, H2O.1, H2O.1 MN.21: 6 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 Chain C: Y.30 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 MN.22: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adair, B.D. et al., Structure-guided design of pure orthosteric inhibitors of alpha IIb beta 3 that prevent thrombosis but preserve hemostasis. Nat Commun (2020)

Release Date

2019-12-11

Peptides

Integrin alpha-V: A
Integrin beta-3: B
Fibronectin, HR10 variant: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-V

Integrin beta-3

Fibronectin, HR10 variant

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