SMTL ID : 6msl.1

Integrin AlphaVBeta3 ectodomain bound to EETI-II 2.5D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN: 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-MAN.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-BMA-MAN.4: 8 residues within 4Å: Chain A: E.448, Y.450, P.451, N.458, T.460, C.461, C.472, N.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.448

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.2: 4 residues within 4Å: Chain A: D.257, K.259, N.260, S.262 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: A.584, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: T.942, N.943 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: D.751, I.869, S.919, N.950 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: N.99, N.371, S.398, I.399, E.400 Ligands: NAG.17 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.3: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, Y.254, S.263, L.264, Y.265, 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.9: 6 residues within 4Å: Chain A: D.621, P.624 Chain B: Y.531, Y.557, N.559, C.583 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: Q.494, N.524, D.564 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain A: N.821, Q.885, G.887 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.821 NAG.17: 3 residues within 4Å: Chain B: K.98, N.99 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG.18: 4 residues within 4Å: Chain A: R.248 Chain B: N.316, L.317, N.320 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.316, B:L.317 Hydrogen bonds: B:N.320, A:R.248

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

MN.12: 6 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.237, 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.351, A:D.353, A:D.353, A:F.355, A:D.357 MN.15: 7 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, P.420, D.421, A.437 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:C.596, A:D.599, A:D.599, A:V.601, A:E.636 MN.19: 5 residues within 4Å: Chain B: S.121, S.123, A.218, E.220 Chain C: D.7 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:S.121, B:S.123, B:E.220, C:D.7, H2O.1 MN.20: 4 residues within 4Å: Chain B: S.123, D.126, D.127, D.251 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.127, B:D.251, B:D.251 MN.21: 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

Van Agthoven, J.F. et al., Structural Basis of the Differential Binding of Engineered Knottins to Integrins alpha V beta 3 and alpha 5 beta 1. Structure (2019)

Release Date

2019-10-23

Peptides

Integrin alpha-V: A
Integrin beta-3: B
Cystine Knot Protein 2.5D: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-V

Integrin beta-3

Cystine Knot Protein 2.5D

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