SMTL ID : 5nay.1

Crystal structures of homooligomers of collagen type IV. alpha1NC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 7 residues within 4Å: Chain A: A.74, S.75, R.76, N.77, D.78, G.178 Chain D: R.179 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: Y.189 Chain C: F.64, N.66 Chain F: Y.185, A.186 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: Y.185, A.186 Chain D: F.64, N.66 Chain F: Y.189 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: F.64, N.66 Chain B: Y.189 Chain D: Y.185, A.186 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain B: A.74, S.75, R.76, N.77, D.78, G.178 Chain E: R.179 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: F.64, N.66 Chain C: Y.189 Chain E: Y.185, A.186 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: Y.185, A.186 Chain D: Y.189 Chain E: F.64, N.66 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain C: Y.185, A.186 Chain E: Y.189 Chain F: F.64, N.66 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain C: A.74, S.75, R.76, N.77, D.78, G.178 Chain F: R.179 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain A: R.179 Chain D: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain B: R.179 Chain E: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.19: 7 residues within 4Å: Chain C: R.179 Chain F: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: A.212, G.213, E.214, L.215, R.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.213, A:L.215, A:R.216 Salt bridges: A:R.216 SO4.9: 5 residues within 4Å: Chain B: A.212, G.213, E.214, L.215, R.216 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.213, B:L.215, B:R.216 Water bridges: B:T.217 Salt bridges: B:R.216 SO4.12: 5 residues within 4Å: Chain C: A.212, G.213, E.214, L.215, R.216 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.213, C:E.214, C:L.215, C:R.216 Water bridges: C:G.213 Salt bridges: C:R.216 SO4.14: 4 residues within 4Å: Chain D: Y.31, R.102 Chain F: R.198, M.201 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:Y.31, D:Y.31 Salt bridges: D:R.102, F:R.198 Water bridges: F:R.198 SO4.15: 5 residues within 4Å: Chain D: A.212, G.213, E.214, L.215, R.216 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.213, D:E.214, D:L.215, D:R.216 Water bridges: D:T.217 Salt bridges: D:R.216 SO4.17: 5 residues within 4Å: Chain E: A.212, G.213, E.214, L.215, R.216 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.213, E:E.214, E:L.215, E:R.216 Water bridges: E:T.217 Salt bridges: E:R.216 SO4.18: 4 residues within 4Å: Chain D: R.198, M.201 Chain E: Y.31, R.102 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.107 Water bridges: E:Y.31, E:Y.31 Salt bridges: E:R.102, D:R.198 SO4.20: 5 residues within 4Å: Chain F: A.212, G.213, E.214, L.215, R.216 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.213, F:E.214, F:L.215, F:R.216 Water bridges: F:T.217 Salt bridges: F:R.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Casino, P. et al., Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly. IUCrJ (2018)

Release Date

2018-09-12

Peptides

Collagen alpha-1(IV) chain: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Collagen alpha-1(IV) chain

Related Entries With Identical Sequence