SMTL ID : 5naz.1

Crystal structures of homooligomers of collagen type IV. alpha5NC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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.185, A.186 Chain D: F.64, N.66 Chain E: Y.189 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain B: A.74, S.75, R.76, N.77, D.78, G.178 Chain F: R.179 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: Y.185, A.186 Chain D: Y.189 Chain F: F.64, N.66 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain C: A.74, S.75, R.76, N.77, D.78, G.178 Chain E: R.179 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain C: Y.185, A.186 Chain E: F.64, N.66 Chain F: Y.189 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.14: 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.17: 7 residues within 4Å: Chain C: R.179 Chain E: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: Y.189 Chain C: F.64, N.66 Chain E: Y.185, A.186 Ligand excluded by PLIP CL.21: 7 residues within 4Å: Chain B: R.179 Chain F: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain B: F.64, N.66 Chain C: Y.189 Chain F: Y.185, A.186 Ligand excluded by PLIP

12 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 9 residues within 4Å: Chain A: A.186 Chain C: N.66, N.68 Chain D: N.66, I.67, N.68 Chain E: M.93, A.186 Ligands: PG4.19 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.68, C:N.66, C:N.68 Water bridges: D:N.66 PG4.4: 5 residues within 4Å: Chain A: P.86, E.87, Y.184 Chain C: I.67, N.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.86 PG4.7: 9 residues within 4Å: Chain A: N.66, N.68 Chain B: A.186 Chain D: M.93, A.186 Chain F: N.66, I.67, N.68 Ligands: PG4.15 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:N.68, A:N.66, A:N.68 Water bridges: F:N.66 PG4.8: 5 residues within 4Å: Chain A: I.67, N.68 Chain B: P.86, E.87, Y.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.86 PG4.11: 9 residues within 4Å: Chain B: N.66, N.68 Chain C: A.186 Chain E: N.66, I.67, N.68 Chain F: M.93, A.186 Ligands: PG4.23 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:N.68, B:N.66, B:N.68 Water bridges: E:N.66 PG4.12: 5 residues within 4Å: Chain B: I.67, N.68 Chain C: P.86, E.87, Y.184 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.86 PG4.15: 9 residues within 4Å: Chain A: N.66, I.67, N.68 Chain B: M.93, A.186 Chain D: A.186 Chain F: N.66, N.68 Ligands: PG4.7 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:N.66, F:N.68, A:N.68 Water bridges: A:N.66 PG4.16: 5 residues within 4Å: Chain D: P.86, E.87, Y.184 Chain F: I.67, N.68 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.86 PG4.19: 9 residues within 4Å: Chain A: M.93, A.186 Chain C: N.66, I.67, N.68 Chain D: N.66, N.68 Chain E: A.186 Ligands: PG4.3 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.68, D:N.66, D:N.68 Water bridges: C:N.66 PG4.20: 5 residues within 4Å: Chain D: I.67, N.68 Chain E: P.86, E.87, Y.184 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:P.86 PG4.23: 9 residues within 4Å: Chain B: N.66, I.67, N.68 Chain C: M.93, A.186 Chain E: N.66, N.68 Chain F: A.186 Ligands: PG4.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:N.68, E:N.66, E:N.68 Water bridges: B:N.66 PG4.24: 5 residues within 4Å: Chain E: I.67, N.68 Chain F: P.86, E.87, Y.184 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:P.86

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-5(IV) chain: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Collagen alpha-5(IV) chain