SMTL ID : 1t61.1

crystal structure of collagen IV NC1 domain from placenta basement membrane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-4-2-mer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: Y.185, A.186 Chain D: F.64, N.66 Chain E: Y.189 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) K.2: 5 residues within 4Å: Chain A: F.64, N.66 Chain B: Y.189 Chain D: Y.185, A.186 No protein-ligand interaction detected (PLIP) K.8: 5 residues within 4Å: Chain B: F.64, N.66 Chain C: Y.187 Chain F: Y.183, A.184 No protein-ligand interaction detected (PLIP) K.11: 6 residues within 4Å: Chain A: Y.189 Chain C: Y.63, N.65, Y.71 Chain E: Y.185, A.186 No protein-ligand interaction detected (PLIP) K.12: 5 residues within 4Å: Chain C: Y.183, A.184 Chain E: F.64, N.66 Chain F: Y.187 No protein-ligand interaction detected (PLIP) K.19: 6 residues within 4Å: Chain B: Y.185, A.186 Chain D: Y.189 Chain F: Y.63, N.65, Y.71 No protein-ligand interaction detected (PLIP)

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

CL.3: 6 residues within 4Å: Chain A: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain B: A.74, S.75, R.76, N.77, D.78, G.178, R.179 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain C: A.73, S.74, R.75, N.76, D.77 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain D: A.74, S.75, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: R.177 Chain E: A.74, R.76, N.77, D.78, G.178 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain F: A.73, S.74, R.75, N.76, D.77 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Y.28, C.53, L.54, R.55 Chain B: V.120, H.121, Q.123 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.55, A:R.55, B:H.121, B:Q.123 Water bridges: A:R.55 GOL.5: 7 residues within 4Å: Chain A: T.85, P.86, E.87, P.88, M.89, Y.184 Chain C: P.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.85, A:M.89 Water bridges: A:Y.184 GOL.6: 9 residues within 4Å: Chain A: M.89, Y.184, Y.185, A.186 Chain C: P.66, G.67 Chain D: N.66, N.68 Ligands: K.1 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:A.186, D:N.68 Water bridges: C:N.65, C:N.65, C:G.67, C:G.67 GOL.7: 7 residues within 4Å: Chain A: V.120, H.121, Q.123 Chain C: W.27, C.52, L.53, A.54 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:A.54, A:H.121, A:Q.123 GOL.10: 5 residues within 4Å: Chain A: L.63, F.73 Chain B: A.194, T.195, H.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.195, B:H.218 Water bridges: B:T.195 GOL.16: 4 residues within 4Å: Chain D: V.120, H.121 Chain F: W.27, A.54 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.121 GOL.18: 7 residues within 4Å: Chain D: Y.28, C.53, L.54, R.55 Chain E: V.120, H.121, Q.123 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:H.121, E:Q.123, D:R.55, D:R.55

2 x CA: CALCIUM ION(Non-covalent)

CA.14: 2 residues within 4Å: Chain C: D.148, E.149 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.148, C:E.149, H2O.13, H2O.21, H2O.26 CA.21: 3 residues within 4Å: Chain C: D.148 Chain F: D.148, E.149 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.148, F:E.149, H2O.7, H2O.26, H2O.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanacore, R.M. et al., The alpha1.alpha2 network of collagen IV. Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys cross-links. J.Biol.Chem. (2004)

Release Date

2004-09-21

Peptides

Type IV Collagen: ABDE
Type IV Collagen: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

E
E

C
C

F
F

Type IV Collagen

Type IV Collagen

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