SMTL ID : 6fxq.1

Structure of coproheme decarboxylase from Listeria monocytogenes during turnover

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-pentamer

Ligands

5 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: I.62, L.63, G.64, A.67, D.68 Chain B: E.85 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:N.82 Hydrogen bonds: A:D.68, A:D.68 NA.5: 6 residues within 4Å: Chain A: E.85 Chain C: I.62, L.63, G.64, A.67, D.68 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.68, C:D.68 Water bridges: A:N.82, A:N.82 NA.6: 6 residues within 4Å: Chain B: I.62, L.63, G.64, A.67, D.68 Chain E: E.85 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Water bridges: E:N.82, E:N.82 Hydrogen bonds: B:D.68 NA.12: 6 residues within 4Å: Chain C: E.85 Chain D: I.62, L.63, G.64, A.67, D.68 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.62 Water bridges: C:N.82, C:N.82 NA.16: 6 residues within 4Å: Chain D: E.85 Chain E: I.62, L.63, G.64, A.67, D.68 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.85 Water bridges: D:N.82, D:N.82

5 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Non-covalent)

FEC.2: 29 residues within 4Å: Chain A: V.4, E.108, S.110, Y.112, L.113, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, A.181, V.184, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: VOV.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.146, A:I.170, A:Q.186, A:Q.186, A:W.199, A:W.199, A:V.201, A:L.203, A:I.214 Hydrogen bonds: A:W.158, A:W.199, A:S.224 Water bridges: A:E.108, A:Y.112, A:R.171 Salt bridges: A:K.150, A:H.173, A:R.178 Metal complexes: A:H.173 FEC.7: 25 residues within 4Å: Chain B: E.108, L.109, S.110, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: VOV.8 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:Y.146, B:I.170, B:W.199, B:W.199, B:V.201, B:V.201, B:L.203, B:I.214 Hydrogen bonds: B:S.110, B:W.158, B:Q.186, B:S.224 Salt bridges: B:R.132, B:H.173 pi-Cation interactions: B:R.132 Metal complexes: B:H.173 FEC.10: 27 residues within 4Å: Chain C: V.4, S.110, Y.112, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, A.181, V.184, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: VOV.11 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:Y.146, C:W.199, C:W.199, C:V.201, C:L.203, C:I.214 Hydrogen bonds: C:S.110, C:Y.112, C:W.158, C:Q.186, C:S.224 Salt bridges: C:R.132, C:H.173 FEC.13: 28 residues within 4Å: Chain D: V.4, L.109, S.110, Y.112, L.113, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, V.184, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: VOV.14 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:Y.146, D:I.170, D:I.170, D:Q.186, D:W.199, D:V.201, D:L.203, D:I.214 Hydrogen bonds: D:W.158, D:S.224 Water bridges: D:Y.112, D:R.132, D:W.199 Salt bridges: D:R.132, D:K.150, D:H.173 Metal complexes: D:H.173 FEC.17: 25 residues within 4Å: Chain E: E.108, S.110, Y.112, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: VOV.18 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:Y.146, E:I.170, E:W.199, E:W.199, E:V.201, E:L.203, E:I.214 Hydrogen bonds: E:S.110, E:W.158, E:R.178, E:Q.186, E:S.224 Water bridges: E:Y.112 Salt bridges: E:R.132, E:H.173, E:R.178 Metal complexes: E:H.173

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

VOV.3: 30 residues within 4Å: Chain A: V.4, E.108, L.109, S.110, Y.112, L.113, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, V.184, Q.185, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: FEC.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.146, A:I.170, A:Q.186, A:Q.186, A:W.199, A:W.199, A:V.201, A:L.203, A:I.214 Hydrogen bonds: A:S.110, A:S.110, A:W.158, A:S.224 Water bridges: A:Y.112, A:W.199 Salt bridges: A:R.132, A:K.150, A:H.173 Metal complexes: A:H.173 VOV.8: 26 residues within 4Å: Chain B: E.108, L.109, S.110, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, V.184, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: FEC.7 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:Y.146, B:I.170, B:W.199, B:W.199, B:V.201, B:V.201, B:L.203, B:I.214 Hydrogen bonds: B:S.110, B:S.110, B:W.158, B:S.224 Salt bridges: B:R.132, B:H.173 Metal complexes: B:H.173 VOV.11: 27 residues within 4Å: Chain C: V.4, L.109, S.110, Y.112, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, A.181, V.184, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: FEC.10 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:Y.146, C:W.199, C:W.199, C:V.201, C:V.201, C:L.203, C:I.214 Hydrogen bonds: C:W.158, C:S.224 Water bridges: C:Y.112, C:W.199 Salt bridges: C:H.173 Metal complexes: C:H.173 VOV.14: 30 residues within 4Å: Chain D: V.4, E.108, L.109, S.110, Y.112, L.113, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, V.184, Q.185, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: FEC.13 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:Y.146, D:I.170, D:Q.186, D:W.199, D:W.199, D:V.201, D:L.203, D:I.214 Hydrogen bonds: D:E.108, D:S.110, D:W.158, D:S.224 Water bridges: D:Y.112, D:I.188, D:W.199 Salt bridges: D:K.150, D:H.173 Metal complexes: D:H.173 VOV.18: 28 residues within 4Å: Chain E: E.108, L.109, S.110, Y.112, R.132, Y.146, M.148, K.150, W.158, I.170, H.173, G.174, G.177, R.178, Y.180, V.184, Q.185, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 Ligands: FEC.17 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:Y.146, E:I.170, E:W.199, E:W.199, E:V.201, E:L.203, E:I.214 Hydrogen bonds: E:S.110, E:S.110, E:W.158, E:S.224 Water bridges: E:Y.112 Salt bridges: E:R.132, E:H.173 Metal complexes: E:H.173

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

MPD.4: 11 residues within 4Å: Chain A: E.79, N.82, E.83, N.86 Chain C: S.61, N.237, L.238, L.239, Q.243, K.246, L.247 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.247, A:E.79, A:N.86 Hydrogen bonds: C:L.238 MPD.9: 10 residues within 4Å: Chain A: S.61, N.237, L.239, Q.243, K.246, L.247 Chain B: E.79, N.82, E.83, N.86 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.79, B:N.86, A:L.247 MPD.15: 11 residues within 4Å: Chain C: E.79, N.82, E.83, N.86 Chain D: S.61, N.237, L.238, L.239, Q.243, K.246, L.247 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:N.82, D:N.237 Hydrophobic interactions: D:Q.243, D:K.246 MPD.19: 10 residues within 4Å: Chain B: S.61, N.237, L.239, Q.243, K.246, L.247 Chain E: E.79, N.82, E.83, N.86 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:L.247, E:E.79, E:E.83, E:N.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milazzo, L. et al., Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb. Acs Catalysis (2019)

Release Date

2019-07-10

Peptides

Putative heme-dependent peroxidase lmo2113: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Putative heme-dependent peroxidase lmo2113

Related Entries With Identical Sequence