SMTL ID : 8bbv.1

Coproporphyrin III - LmCpfC complex soaked 2min with Fe2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Y.64, Y.82, I.83, P.90, A.95, A.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.83, A:I.83

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: Q.220, S.221, E.222, D.233, V.234, Q.235, D.267, E.271, C.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.221, A:E.222, A:E.271 EDO.3: 5 residues within 4Å: Chain A: K.4, D.75, E.76, V.77, E.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.75

1 x HT9: coproporphyrin III(Non-covalent)

HT9.4: 33 residues within 4Å: Chain A: Y.12, G.13, T.14, P.15, Y.24, Y.25, I.28, R.29, H.30, L.42, R.45, Y.46, S.53, L.55, A.113, F.119, S.120, Y.124, H.182, S.183, L.184, P.185, Y.195, G.223, K.224, T.225, W.229, F.257, H.261, L.262, E.263 Ligands: FE2.5, CL.6 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.12, A:Y.12, A:Y.12, A:Y.12, A:Y.24, A:Y.25, A:I.28, A:L.42, A:A.113, A:H.182, A:W.229, A:L.262, A:E.263 Hydrogen bonds: A:T.14, A:Y.46, A:S.53, A:Y.124, A:K.224, A:L.262 Water bridges: A:Y.12, A:H.182 Salt bridges: A:R.29, A:H.30, A:R.45 pi-Stacking: A:H.182

1 x FE2: FE (II) ION(Non-covalent)

FE2.5: 3 residues within 4Å: Chain A: Y.12, H.182 Ligands: HT9.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.12

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

CL.6: 4 residues within 4Å: Chain A: Y.12, K.86, H.87 Ligands: HT9.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabler, T. et al., Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species. Protein Sci. (2023)

Release Date

2023-01-11

Peptides

Coproporphyrin III ferrochelatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Coproporphyrin III ferrochelatase

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