SMTL ID : 3hnj.1

Crystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:L.10, A:N.11, A:L.14, A:P.45, A:F.65, A:F.65, A:F.65, A:L.68, A:L.68, A:R.106 Hydrogen bonds: A:E.8 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEM.3: 21 residues within 4Å: Chain B: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, I.97, C.98, C.101, H.102, Y.105, R.106 Ligands: ZN.6 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:N.11, B:P.45, B:F.65, B:L.68, B:L.94, B:R.106 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEM.7: 19 residues within 4Å: Chain C: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:N.11, C:L.14, C:P.45, C:F.61, C:F.65, C:F.65, C:L.68, C:R.106 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEM.9: 20 residues within 4Å: Chain D: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, I.97, C.98, C.101, H.102, Y.105, R.106 Ligands: ZN.12 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:L.10, D:N.11, D:P.45, D:F.61, D:F.65, D:F.65, D:L.68, D:R.106 Metal complexes: D:H.102

8 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 4 residues within 4Å: Chain A: H.73, H.77 Chain C: D.74 Chain D: H.63 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Metal complexes: A:H.73, A:H.77, C:D.74, C:D.74, D:H.63 ZN.4: 4 residues within 4Å: Chain B: H.73, H.77 Chain C: H.63 Chain D: D.74 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Metal complexes: B:H.73, B:H.77, C:H.63, D:D.74 ZN.5: 1 residues within 4Å: Chain B: D.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.5, H2O.3, H2O.3, H2O.3, H2O.4 ZN.6: 1 residues within 4Å: Ligands: HEM.3 No protein-ligand interaction detected (PLIP) ZN.8: 4 residues within 4Å: Chain A: D.74 Chain B: H.63 Chain C: H.73, H.77 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.74, C:H.73, C:H.77, B:H.63 ZN.10: 4 residues within 4Å: Chain A: H.63 Chain B: D.74 Chain D: H.73, H.77 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B Metal complexes: A:H.63, D:H.73, D:H.77, B:D.74 ZN.11: 2 residues within 4Å: Chain D: D.2, D.5 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.5, H2O.7, H2O.7, H2O.7, H2O.8 ZN.12: 1 residues within 4Å: Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgado, E.N. et al., Metal templated design of protein interfaces. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-02-09

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562