SMTL ID : 7rww.1

Crystal structure of a Zn-bound RIDC1 variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.77, E.81 Chain D: H.77, E.81 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.77, A:E.81, H2O.8 ZN.2: 3 residues within 4Å: Chain A: A.1, N.6, D.39 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.1, A:D.39, A:D.39 ZN.3: 3 residues within 4Å: Chain A: H.59 Chain B: H.73, H.77 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.73, A:H.59, H2O.5, H2O.5 ZN.8: 6 residues within 4Å: Chain B: H.77, E.81 Chain C: H.77, L.78, E.81, K.83 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Metal complexes: C:H.77, B:H.77, B:E.81, B:E.81 ZN.13: 1 residues within 4Å: Chain D: H.59 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.59, H2O.7, H2O.8

4 x HEC: HEME C(Non-covalent)(Covalent)

HEC.4: 21 residues within 4Å: Chain A: 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, L.94, 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:L.14, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:R.106 Water bridges: A:E.4 pi-Cation interactions: A:H.102 Metal complexes: A:H.102 HEC.7: 21 residues within 4Å: Chain B: 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, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:L.10, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Water bridges: B:R.106, B:R.106, B:R.106, B:R.106 pi-Stacking: B:H.102, B:H.102 Metal complexes: B:H.102 HEC.11: 21 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, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:N.11, C:L.14, C:P.45, C:F.61, C:F.65, C:F.65, C:L.68, C:R.106, C:R.106 Salt bridges: C:R.106 pi-Stacking: C:H.102 Metal complexes: C:H.102 HEC.14: 21 residues within 4Å: Chain D: 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, L.94, T.97, 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:N.11, D:L.14, D:P.45, D:F.65, D:F.65, D:F.65, D:R.106 pi-Stacking: D:H.102, D:H.102 Metal complexes: D:H.102

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 11 residues within 4Å: Chain B: I.67, Q.71, Q.93, L.94, C.96, T.97, A.100 Chain D: I.67, Q.71, T.97 Ligands: MPD.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.67, B:Q.93, B:A.100 Hydrogen bonds: B:Q.71, D:Q.71 MPD.6: 11 residues within 4Å: Chain A: W.66 Chain B: W.66, I.67, G.70, Q.71, A.74 Chain C: W.66 Chain D: H.63, W.66 Ligands: MPD.5, EPE.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.66, D:W.66 Water bridges: B:Q.71, D:H.63 MPD.10: 8 residues within 4Å: Chain C: W.41, S.42, P.53, D.54, H.59, R.62 Chain D: T.31, A.35 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.53 Water bridges: C:R.62, D:A.35, D:A.35

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.9: 10 residues within 4Å: Chain A: I.67, Q.71, T.97 Chain C: I.67, Q.71, Q.93, C.96, T.97, A.100 Ligands: EPE.12 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.67, C:Q.93, A:Q.71 Hydrogen bonds: C:T.97, A:Q.71 Water bridges: A:Q.71

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 14 residues within 4Å: Chain A: H.63, W.66, I.67, G.70, Q.71 Chain B: W.66 Chain C: W.66, I.67, G.70, Q.71, A.74 Chain D: W.66 Ligands: MPD.6, MRD.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakkis, A. et al., Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Chem.Commun.(Camb.) (2022)

Release Date

2022-06-29

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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