SMTL ID : 4jea.1

Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide bonds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 15 residues within 4Å: Chain A: E.4, M.7, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.14, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:R.106 Hydrogen bonds: A:E.4 Water bridges: A:E.8, A:R.106 pi-Stacking: A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEM.4: 14 residues within 4Å: Chain B: E.4, M.7, N.11, M.33, P.45, 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:M.7, B:N.11, B:P.45, B:F.61, B:F.65, B:F.65, B:R.106 Water bridges: B:E.4 pi-Stacking: B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEM.7: 16 residues within 4Å: Chain C: E.4, M.7, E.8, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:M.7, C:N.11, C:L.14, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:R.106 Hydrogen bonds: C:E.8, C:E.8 Water bridges: C:E.4, C:E.4, C:E.4 pi-Stacking: C:H.102, C:H.102 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEM.11: 16 residues within 4Å: Chain D: E.4, M.7, E.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, 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:N.11, D:P.45, D:F.65, D:F.65, D:F.65, D:R.106 pi-Stacking: D:H.102, D:H.102 pi-Cation interactions: D:R.106, D:R.106 Metal complexes: D:H.102

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.73, H.77 Chain B: H.63 Chain D: D.74 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 interactions with chain A Metal complexes: D:D.74, D:D.74, B:H.63, A:H.73, A:H.77 ZN.5: 4 residues within 4Å: Chain A: H.63 Chain B: H.73, H.77 Chain C: D.74 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.73, B:H.77, C:D.74, C:D.74, A:H.63 ZN.8: 4 residues within 4Å: Chain B: D.74 Chain C: H.73, H.77 Chain D: H.63 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.74, B:D.74, C:H.73, C:H.77, D:H.63 ZN.12: 4 residues within 4Å: Chain A: D.74 Chain C: H.63 Chain D: H.73, H.77 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 interactions with chain A Metal complexes: D:H.73, D:H.77, C:H.63, A:D.74, A:D.74

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: A.38, W.41, I.69 Chain B: A.34 No protein-ligand interaction detected (PLIP) SO4.6: 2 residues within 4Å: Chain A: A.38 Chain B: A.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.38 SO4.9: 4 residues within 4Å: Chain B: H.73, D.74 Chain C: H.73, D.74 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:H.73 Salt bridges: B:H.73, C:H.73 SO4.10: 4 residues within 4Å: Chain C: A.38, W.41, W.66, I.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.66 SO4.13: 4 residues within 4Å: Chain A: H.73, D.74 Chain D: H.73, D.74 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Water bridges: A:G.70 Salt bridges: A:H.73, D:H.73 SO4.14: 4 residues within 4Å: Chain C: A.34 Chain D: A.38, W.41, W.66 No protein-ligand interaction detected (PLIP) SO4.15: 4 residues within 4Å: Chain C: H.77 Chain D: H.59, H.63, W.66 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:N.80, D:H.59 Salt bridges: C:H.77, D:H.63

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
C

D
D

soluble cytochrome b562

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