SMTL ID : 8tcg.1

Integrin alpha-v beta-6 in complex with minibinder B6_BP_dslf

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 10 residues within 4Å: Chain A: T.212, A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, Y.265, N.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.214 Hydrophobic interactions: A:A.213

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: D.284, I.285, N.286, D.288, Y.290, D.292, Q.320 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.284, A:D.288, A:D.288, A:Y.290, A:D.292 CA.3: 7 residues within 4Å: Chain A: D.349, L.350, D.351, D.353, F.355, D.357, N.377 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.4: 7 residues within 4Å: Chain A: D.414, I.415, 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.5: 7 residues within 4Å: Chain A: D.230, F.231, N.232, D.234, I.236, D.238, G.258 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

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

NAG.6: 5 residues within 4Å: Chain A: E.15, G.16, N.44, V.51, E.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.44, A:E.52 NAG.7: 4 residues within 4Å: Chain A: D.257, K.259, N.260, S.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.259, A:N.260

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

MN.8: 6 residues within 4Å: Chain B: S.15, M.16, D.18, D.19, D.142 Chain C: E.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.15, B:D.18, B:D.18, B:D.19, B:D.142 MN.9: 5 residues within 4Å: Chain B: S.13, S.15, N.106, E.111 Chain C: D.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.13, B:S.15, B:E.111, C:D.10 MN.10: 8 residues within 4Å: Chain B: E.50, N.106, D.108, T.109, P.110, E.111, H.146 Chain C: D.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.50, B:D.108, B:D.108, B:P.110

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-6: B
Minibinder B6_BP_dslf: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-V heavy chain

Integrin beta-6

Minibinder B6_BP_dslf