SMTL ID : 5loq.1

Structure of coproheme bound HemQ from Listeria monocytogenes

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 A, 2 interactions with chain B Hydrogen bonds: A:D.68, B:E.85 Water bridges: B:N.82 NA.4: 6 residues within 4Å: Chain B: I.62, L.63, G.64, A.67, D.68 Chain E: E.85 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:D.68 Water bridges: E:N.82, E:N.82 NA.7: 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 A, 2 interactions with chain C Water bridges: A:N.82, A:N.82 Hydrogen bonds: C:D.68, C:D.68 NA.9: 6 residues within 4Å: Chain C: E.85 Chain D: I.62, L.63, G.64, A.67, D.68 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:N.82, C:N.82 Hydrogen bonds: D:G.64, D:D.68 NA.12: 6 residues within 4Å: Chain D: E.85 Chain E: I.62, L.63, G.64, A.67, D.68 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Water bridges: D:N.82, D:N.82 Hydrogen bonds: E:D.68

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, 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.146, A:I.170, A:Q.186, A:W.199, A:V.201, A:L.203, A:I.214 Hydrogen bonds: A:E.108, A:S.110, A:Y.146, A:W.158, A:Q.186, A:S.224, A:S.224 Water bridges: A:Y.112, A:W.199, A:R.219 Salt bridges: A:R.132, A:K.150 Metal complexes: A:H.173 FEC.5: 27 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, A.181, V.184, Q.185, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:Y.146, B:I.170, B:Q.186, B:Q.186, B:W.199, B:W.199, B:V.201, B:V.201, B:L.203, B:I.214 Hydrogen bonds: B:W.158, B:Y.180, B:Q.186, B:S.224 Water bridges: B:K.183 Salt bridges: B:R.132, B:H.173 Metal complexes: B:H.173 FEC.8: 29 residues within 4Å: Chain C: V.4, E.108, S.110, N.111, 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.185, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, A.228, F.230 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.146, C:I.170, C:Q.186, C:W.199, C:W.199, C:V.201, C:L.203, C:I.214 Hydrogen bonds: C:S.110, C:Y.112, C:Y.112, C:W.158, C:Y.180, C:S.224 Water bridges: C:R.132, C:V.215 Salt bridges: C:H.173 FEC.10: 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, R.219, S.224, F.230 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:Y.146, D:I.170, D:W.199, D:L.203, D:I.214 Hydrogen bonds: D:L.113, D:Y.146, D:Y.146, D:W.158, D:Q.186, D:S.224 Water bridges: D:Y.112, D:R.132, D:W.199, D:R.219 Salt bridges: D:R.132, D:K.150 Metal complexes: D:H.173 FEC.13: 29 residues within 4Å: Chain E: E.108, L.109, S.110, N.111, 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.185, Q.186, I.188, W.199, V.201, L.203, I.214, V.215, M.218, S.224, F.230 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:I.170, E:Q.186, E:Q.186, E:W.199, E:W.199, E:V.201, E:L.203, E:I.214 Hydrogen bonds: E:S.110, E:Y.112, E:W.158, E:G.177, E:Q.186, E:S.224 Water bridges: E:Y.112, E:V.215 Salt bridges: E:H.173 Metal complexes: E:H.173

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

MPD.3: 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 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:K.246, C:L.247, A:E.79, A:N.86 Hydrogen bonds: C:S.61, C:L.238 MPD.6: 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: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.247, B:E.79, B:N.86 MPD.11: 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.14: 11 residues within 4Å: Chain B: S.61, N.237, L.238, L.239, Q.243, K.246, L.247 Chain E: E.79, N.82, E.83, N.86 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:E.79, E:E.83, E:N.86, B:L.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofbauer, S. et al., Hydrogen peroxide-mediated conversion of coproheme to heme b by HemQ-lessons from the first crystal structure and kinetic studies. FEBS J. (2016)

Release Date

2016-10-26

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

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