SMTL ID : 9han.1

Bovine collagen VI local refinement of C-terminal region

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain B: N.895, Y.896, T.897 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.895 NAG-NAG-FUC.4: 3 residues within 4Å: Chain E: N.895, Y.896, T.897 No protein-ligand interaction detected (PLIP)

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: 3 residues within 4Å: Chain C: N.905, T.907, V.908 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain C: T.960, N.962, D.989, D.991, V.992 Chain E: S.841, H.842, D.845 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.842 NAG-NAG.5: 6 residues within 4Å: Chain B: S.841, H.842, D.845 Chain F: N.962, D.963, D.991 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.842, B:D.845

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.6: 3 residues within 4Å: Chain F: N.905, T.907, V.908 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: I.2386, N.2387, T.2389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.2389 NAG.8: 3 residues within 4Å: Chain D: I.2386, N.2387, T.2389 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.2389, D:T.2389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godwin, A.R.F. et al., Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations. Nat Commun (2025)

Release Date

2025-08-20

Peptides

Collagen type VI alpha 3 chain: AD
Collagen type VI alpha 1 chain: BE
Collagen type VI alpha 2 chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
F

B
A

E
D

C
B

F
E

Collagen type VI alpha 3 chain

Collagen type VI alpha 1 chain

Collagen type VI alpha 2 chain