SMTL ID : 6fxj.1

Structure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-pentamer

Ligands

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

NA.1: 7 residues within 4Å: Chain A: I.63, L.64, G.65, A.68, D.69 Chain B: N.83, E.86 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:N.83 Hydrogen bonds: A:D.69, A:D.69 NA.3: 6 residues within 4Å: Chain A: E.86 Chain C: I.63, L.64, G.65, A.68, D.69 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.69, C:D.69 Water bridges: C:I.63 NA.4: 7 residues within 4Å: Chain B: I.63, L.64, G.65, A.68, D.69 Chain E: N.83, E.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.63, B:D.69 Water bridges: B:I.63 NA.12: 4 residues within 4Å: Chain C: M.47, T.50, R.76, V.85 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.50, C:T.50, C:R.76, C:R.76 NA.13: 6 residues within 4Å: Chain C: E.86 Chain D: I.63, L.64, G.65, A.68, D.69 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.63, D:D.69 Water bridges: D:I.63 NA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.20: 6 residues within 4Å: Chain D: E.86 Chain E: I.63, L.64, G.65, A.68, D.69 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.86 Water bridges: E:I.63

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

FEC.2: 23 residues within 4Å: Chain A: S.111, Y.113, L.114, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:L.114, A:Y.147, A:I.171, A:L.204 Hydrogen bonds: A:W.159, A:Q.187, A:W.200, A:S.225 Water bridges: A:Y.113, A:H.174, A:H.174 Salt bridges: A:K.151, A:H.174, A:R.179 Metal complexes: A:H.174 FEC.5: 22 residues within 4Å: Chain B: L.110, S.111, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:Q.187, B:W.200, B:W.200, B:V.202, B:L.204, B:I.215 Hydrogen bonds: B:S.111, B:Y.147, B:W.159, B:S.225, B:S.225 Water bridges: B:W.200, B:R.220 Salt bridges: B:R.133, B:R.133, B:K.151 FEC.8: 24 residues within 4Å: Chain C: S.111, Y.113, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, A.182, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Q.187, C:I.189, C:W.200, C:V.202, C:V.202, C:I.215 Hydrogen bonds: C:Y.147, C:Y.147, C:W.159 Water bridges: C:Y.113, C:W.200 Salt bridges: C:R.133, C:R.133, C:K.151, C:H.174 pi-Stacking: C:H.174, C:H.174 FEC.14: 24 residues within 4Å: Chain D: S.111, Y.113, L.114, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:Y.147, D:I.171, D:Q.187, D:W.200, D:L.204, D:F.231 Hydrogen bonds: D:W.159, D:Q.187, D:W.200, D:S.225 Water bridges: D:E.109, D:E.109, D:Y.113, D:H.174, D:H.174, D:R.179 Salt bridges: D:R.133, D:K.151, D:H.174, D:R.179, D:R.179 Metal complexes: D:H.174 FEC.21: 25 residues within 4Å: Chain E: V.5, L.110, S.111, Y.113, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231 19 PLIP interactions: 19 interactions with chain E, Hydrophobic interactions: E:I.171, E:I.171, E:Q.187, E:W.200, E:V.202, E:L.204, E:I.215 Hydrogen bonds: E:Y.147, E:W.159, E:S.225, E:S.225 Water bridges: E:Y.113, E:Y.113, E:R.220 Salt bridges: E:R.133, E:K.151, E:R.179, E:R.179 Metal complexes: E:H.174

10 x POL: N-PROPANOL(Non-covalent)

POL.6: 4 residues within 4Å: Chain B: K.67, Y.102, S.233, F.235 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.102 POL.7: 5 residues within 4Å: Chain A: G.232, S.233 Chain B: D.197, Y.198, E.230 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.233 POL.9: 3 residues within 4Å: Chain C: Y.102, S.233, F.235 1 PLIP interactions: 1 interactions with chain C Water bridges: C:T.101 POL.10: 6 residues within 4Å: Chain C: S.150, D.197, Y.198 Chain D: F.231, G.232, S.233 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:S.233 Hydrophobic interactions: C:Y.198 POL.11: 4 residues within 4Å: Chain C: L.8, Q.126, N.127, V.130 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.127 POL.15: 3 residues within 4Å: Chain D: P.100, T.101 Ligands: POL.17 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.101 POL.16: 2 residues within 4Å: Chain D: D.197, Y.198 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.197 POL.17: 6 residues within 4Å: Chain D: K.67, T.101, Y.102, S.233, F.235 Ligands: POL.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.67 POL.22: 4 residues within 4Å: Chain E: K.67, Y.102, S.233, F.235 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.102 POL.23: 3 residues within 4Å: Chain E: S.150, D.197, Y.198 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.198

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.19: 1 residues within 4Å: Chain D: R.179 Ligand excluded by PLIP

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