SMTL ID : 8tcf.1

Integrin alpha-v beta-8 in complex with minibinder B8_BP_dsulf

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.1: 12 residues within 4Å: Chain A: A.213, Q.214, F.217, Y.254, S.263, L.264, Y.265, N.266 Chain C: R.6, N.8, E.41, E.71 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.217 Hydrogen bonds: A:Q.214

3 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: 6 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: E.29, I.303, R.309, N.328 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: T.13, Q.14, L.39, Y.42, N.348, E.349 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.39

5 x CA: CALCIUM ION(Non-covalent)

CA.5: 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 CA.6: 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 CA.7: 6 residues within 4Å: Chain A: D.414, D.416, N.418, Y.420, D.422, A.438 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.414, A:D.416, A:Y.420, A:D.422, A:D.422 CA.8: 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.234, A:D.234, A:I.236, A:D.238, A:D.238 CA.10: 5 residues within 4Å: Chain B: D.90, N.146, D.148, P.150, E.151 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:D.148, B:D.148, B:P.150

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

NAG.9: 2 residues within 4Å: Chain A: N.260, S.262 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain B: N.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.130 NAG.13: 4 residues within 4Å: Chain B: Y.297, N.299, T.301, P.311 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.297 Hydrogen bonds: B:T.301 NAG.14: 3 residues within 4Å: Chain B: D.306, R.317, N.318 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.317 Hydrogen bonds: B:D.306, B:N.318

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain B: S.53, S.55, E.151 Chain C: D.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.53, B:S.55, B:E.151, C:D.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, A. et al., De novo design of highly selective miniprotein inhibitors of integrins alpha v beta 6 and alpha v beta 8. Nat Commun (2023)

Release Date

2023-09-27

Peptides

Integrin alpha-V heavy chain: A
Integrin beta-8: B
Minibinder B8_BP_dslf: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-V heavy chain

Integrin beta-8

Minibinder B8_BP_dslf