SMTL ID : 5l32.1

Crystal structure of the Zn-RIDC1 complex bearing six interfacial disulfide bonds

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 17 residues within 4Å: Chain A: L.3, E.4, M.7, E.8, N.11, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:P.45, A:F.65, A:F.65, A:L.68, A:R.106 Hydrogen bonds: A:E.4, A:E.8 pi-Stacking: A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.6: 15 residues within 4Å: Chain B: L.3, E.4, M.7, L.10, N.11, L.14, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:L.10, B:N.11, B:F.61, B:F.65, B:F.65, B:R.106 Hydrogen bonds: B:E.4 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.8: 17 residues within 4Å: Chain C: E.4, M.7, E.8, L.10, N.11, M.33, P.45, P.46, F.61, F.65, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:M.7, C:P.45, C:F.65, C:L.94, C:R.106 Hydrogen bonds: C:E.8 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.9: 16 residues within 4Å: Chain D: E.4, M.7, L.10, N.11, L.14, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:M.7, D:L.10, D:N.11, D:L.14, D:F.65, D:F.65, D:L.68, D:R.106 Hydrogen bonds: D:E.4 pi-Cation interactions: D:R.106 Metal complexes: D:H.102

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 8 residues within 4Å: Chain A: E.92, K.95, C.96, N.99, Q.103 Chain B: E.92, K.95, C.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.92, A:Q.103

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.73, H.77 Chain C: H.63 Chain D: D.74 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C Metal complexes: A:H.73, A:H.77, D:D.74, C:H.63 ZN.4: 4 residues within 4Å: Chain A: H.63 Chain B: D.74 Chain C: H.73, H.77 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Metal complexes: B:D.74, A:H.63, C:H.73, C:H.77 ZN.5: 4 residues within 4Å: Chain A: D.74 Chain B: H.63 Chain D: H.73, H.77 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain A Metal complexes: B:H.63, D:H.73, D:H.77, A:D.74 ZN.7: 4 residues within 4Å: Chain B: H.73, H.77 Chain C: D.74 Chain D: H.63 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Metal complexes: C:D.74, B:H.73, B:H.77, D:H.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Churchfield, L.A. et al., De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J.Am.Chem.Soc. (2016)

Release Date

2016-11-09

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562

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