SMTL ID : 6xub.1

Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-pentamer

Ligands

5 x VOV: harderoheme (III)(Non-covalent)

VOV.1: 30 residues within 4Å: Chain A: A.114, E.115, F.116, N.117, H.120, Y.137, F.139, R.141, W.145, Y.146, R.153, L.157, H.160, G.161, A.164, R.165, F.167, V.170, A.172, T.174, W.185, L.187, F.189, L.200, M.201, M.204, R.205, R.210, V.213, E.216 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:A.114, A:H.120, A:F.139, A:F.139, A:A.164, A:W.185, A:W.185, A:L.187, A:F.189, A:F.189, A:L.200, A:L.200 Hydrogen bonds: A:E.115, A:F.116, A:N.117, A:W.145 Salt bridges: A:R.141, A:H.160, A:R.210 pi-Stacking: A:H.120 Metal complexes: A:H.160 VOV.2: 27 residues within 4Å: Chain B: A.114, E.115, F.116, N.117, H.120, Y.137, F.139, R.141, W.145, R.153, L.157, H.160, G.161, A.164, F.167, V.170, A.172, T.174, W.185, L.187, F.189, L.200, M.201, M.204, R.205, R.210, E.216 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:H.120, B:F.139, B:L.157, B:A.164, B:W.185, B:W.185, B:L.187, B:F.189, B:F.189, B:L.200 Hydrogen bonds: B:E.115, B:F.116, B:N.117, B:W.145 Water bridges: B:H.160, B:R.210 Salt bridges: B:R.141, B:H.160, B:R.210 pi-Stacking: B:H.120 Metal complexes: B:H.160 VOV.3: 27 residues within 4Å: Chain C: A.114, E.115, F.116, N.117, H.120, Y.137, F.139, R.141, W.145, R.153, L.157, H.160, G.161, A.164, F.167, V.170, A.172, T.174, W.185, L.187, F.189, L.200, M.201, M.204, R.210, V.213, E.216 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:H.120, C:F.139, C:F.139, C:L.157, C:A.164, C:W.185, C:L.187, C:F.189, C:F.189, C:L.200, C:L.200 Hydrogen bonds: C:E.115, C:F.116, C:N.117, C:W.145 Water bridges: C:H.160 Salt bridges: C:R.141, C:H.160, C:R.210 pi-Stacking: C:H.120 Metal complexes: C:H.160 VOV.4: 29 residues within 4Å: Chain D: A.114, E.115, F.116, N.117, H.120, Y.137, F.139, R.141, W.145, Y.146, R.153, L.157, H.160, G.161, A.164, R.165, F.167, V.170, A.172, T.174, W.185, L.187, F.189, L.200, M.201, M.204, R.210, V.213, E.216 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:A.114, D:H.120, D:F.139, D:F.139, D:L.157, D:A.164, D:W.185, D:L.187, D:F.189, D:F.189, D:L.200, D:L.200 Hydrogen bonds: D:E.115, D:F.116, D:N.117, D:W.145 Water bridges: D:M.204 Salt bridges: D:R.141, D:H.160, D:R.210 pi-Stacking: D:H.120 Metal complexes: D:H.160 VOV.5: 27 residues within 4Å: Chain E: A.114, E.115, F.116, N.117, H.120, Y.137, F.139, R.141, W.145, R.153, L.157, H.160, G.161, A.164, F.167, V.170, A.172, T.174, W.185, L.187, F.189, L.200, M.201, M.204, R.210, V.213, E.216 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:A.114, E:H.120, E:F.139, E:F.139, E:L.157, E:A.164, E:T.174, E:W.185, E:L.187, E:F.189, E:F.189, E:L.200 Hydrogen bonds: E:E.115, E:F.116, E:N.117, E:W.145 Water bridges: E:H.160 Salt bridges: E:R.141, E:H.160, E:R.210 pi-Stacking: E:H.120 Metal complexes: E:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michlits, H. et al., Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation. Acs Catalysis (2020)

Release Date

2020-04-22

Peptides

Chlorite dismutase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Chlorite dismutase

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