SMTL ID : 9iuj.1

Integrin alpha-v beta-3 in complex with rhodostomin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 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.1: 7 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain A: Y.450, P.451, N.458, T.460, C.461, C.472, N.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.450, A:Y.450, A:Y.450 Hydrophobic interactions: A:Y.450

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.2: 4 residues within 4Å: Chain A: D.257, K.259, N.260, S.262 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: F.558, P.583, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: R.248, M.272 Chain B: L.317, N.320 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: S.369, N.371, V.379, S.398, 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: T.212, A.213, Q.214, F.217, 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

7 x CA: CALCIUM ION(Non-covalent)

CA.8: 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:V.601, A:E.636, A:E.636 CA.9: 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 CA.10: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.284, A:Y.290, A:D.292, A:D.292 CA.11: 4 residues within 4Å: Chain A: D.349, D.351, F.355, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:F.355, A:D.357, A:D.357 CA.12: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421 CA.15: 4 residues within 4Å: Chain B: S.123, D.126, D.127, D.251 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.127, B:D.251 CA.16: 6 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220, H.255 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.158, B:D.217, B:D.217, B:P.219

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

NAG.13: 1 residues within 4Å: Chain A: N.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.524 NAG.17: 2 residues within 4Å: Chain B: N.99 Ligands: NAG-NAG.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.98, B:K.98

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 5 residues within 4Å: Chain B: S.121, S.123, E.220, D.251 Chain C: D.51 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.121, B:S.123, B:E.220, C:D.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.T. et al., Integrin alpha-v beta-3 in complex with rhodostomin. To Be Published

Release Date

2025-07-30

Peptides

Integrin alpha-V,Integrin alpha-V,Uncharacterized protein DKFZp686C11235: A
Integrin beta-3,Integrin beta-3,Uncharacterized protein DKFZp686C11235: B
Disintegrin rhodostomin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-V,Integrin alpha-V,Uncharacterized protein DKFZp686C11235

Integrin beta-3,Integrin beta-3,Uncharacterized protein DKFZp686C11235

Disintegrin rhodostomin

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