SMTL ID : 6ujb.1

Integrin alpha-v beta-8 in complex with the Fabs C6D4 and 11D12v2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-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: 9 residues within 4Å: Chain A: T.212, A.213, Q.214, F.217, Y.254, S.263, L.264, Y.265, N.266 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.213, A:F.217 Hydrogen bonds: A:Q.214

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: 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: 2 residues within 4Å: Chain B: N.191, T.193 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: E.90, N.92, I.364, R.370, N.389, T.391 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: T.74, Q.75, L.100, Y.103, N.414 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.100

5 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.7: 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.8: 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 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.234, A:D.234, A:I.236, A:D.238, A:D.238 CA.11: 5 residues within 4Å: Chain B: D.151, N.207, D.209, P.211, E.212 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.151, B:D.209, B:D.209, B:P.211

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

NAG.10: 2 residues within 4Å: Chain A: N.260, S.262 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: N.360, T.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.362 NAG.14: 1 residues within 4Å: Chain B: N.379 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain B: D.112, S.114, S.116, E.212 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.114, B:S.116, B:E.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, M.G. et al., Cryo-EM Reveals Integrin-Mediated TGF-beta Activation without Release from Latent TGF-beta. Cell (2020)

Release Date

2020-02-05

Peptides

Integrin alpha-V: A
Integrin beta-8: B
C6D4 heavy chain Fab: C
C6D4 light chain Fab: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Integrin alpha-V

Integrin beta-8

C6D4 heavy chain Fab

C6D4 light chain Fab

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