SMTL ID : 4jeb.1

Crystal structure of an engineered RIDC1 tetramer with four interfacial disulfide bonds and four three-coordinate Zn(II) sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 14 residues within 4Å: Chain A: E.4, M.7, L.10, N.11, M.33, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:R.106 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEM.4: 15 residues within 4Å: Chain B: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:R.106 pi-Stacking: B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEM.6: 14 residues within 4Å: Chain C: E.4, M.7, L.10, N.11, M.33, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:R.106 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEM.9: 15 residues within 4Å: Chain D: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:M.7, D:L.10, D:L.14, D:P.45, D:F.61, D:F.65, D:F.65, D:F.65, D:R.106 pi-Stacking: D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.73, H.77 Chain B: H.63, W.66 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.73, A:H.77, B:H.63, H2O.1 ZN.3: 1 residues within 4Å: Chain A: D.39 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, H2O.1 ZN.5: 3 residues within 4Å: Chain A: H.63 Chain B: H.73, H.77 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.63, B:H.73, B:H.77, H2O.1 ZN.7: 4 residues within 4Å: Chain C: H.73, H.77 Chain D: H.63, W.66 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.73, C:H.77, D:H.63, H2O.2 ZN.8: 1 residues within 4Å: Chain C: D.39 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, H2O.2 ZN.10: 3 residues within 4Å: Chain C: H.63 Chain D: H.73, H.77 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.73, D:H.77, C:H.63, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medina-Morales, A. et al., In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds. J.Am.Chem.Soc. (2013)

Release Date

2013-08-21

Peptides

soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

soluble cytochrome b562