SMTL ID : 6djp.1

Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.260 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: P.583, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.191 Chain E: G.54 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: S.305 Chain B: N.360, P.372 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.372 NAG-NAG.7: 2 residues within 4Å: Chain B: N.92, N.389 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-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-MAN-MAN-MAN.3: 5 residues within 4Å: Chain A: A.213, S.263, L.264, Y.265, N.266 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.213

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.8: 4 residues within 4Å: Chain B: N.73, T.74, E.233, N.414 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: S.522, K.523, N.524 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:S.522 NAG.10: 1 residues within 4Å: Chain B: N.379 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cormier, A. et al., Cryo-EM structure of the alpha v beta 8 integrin reveals a mechanism for stabilizing integrin extension. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-07-25

Peptides

Integrin alpha-v: A
Integrin beta-8: B
8B8 heavy chain Fab: C
8B8 light chain Fab: D
68 heavy chain Fab: E
68 light chain Fab: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Integrin alpha-v

Integrin beta-8

8B8 heavy chain Fab

8B8 light chain Fab

68 heavy chain Fab

68 light chain Fab