SMTL ID : 8at8.1

Structure of coproporphyrin III-LmCpfC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: Y.12, I.28, K.86, H.87, F.119 Ligands: HT9.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.28 Water bridges: A:K.86, A:K.86 Salt bridges: A:K.86, A:H.87 ACT.2: 4 residues within 4Å: Chain A: K.148, P.150, I.153, F.205 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.205 ACT.3: 1 residues within 4Å: Chain A: D.72 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: Y.25, D.41, R.45, S.221, E.222, G.223, K.224 Ligands: HT9.6, CA.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.25, A:R.45, A:E.222 Water bridges: A:R.45, A:K.224, A:D.267, A:D.267

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

EDO.5: 6 residues within 4Å: Chain A: Y.64, A.81, Y.82, I.83, P.90, A.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.64, A:Y.64, A:I.83

1 x HT9: coproporphyrin III(Non-covalent)

HT9.6: 31 residues within 4Å: Chain A: Y.12, G.13, T.14, P.15, Y.24, Y.25, I.28, R.29, 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, W.229, F.257, H.261, L.262, E.263 Ligands: ACT.1, GOL.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.12, A:Y.12, A:Y.12, A:Y.12, A:Y.12, A:Y.25, A:I.28, A:L.42, A:A.113, A:H.182, A:L.262 Hydrogen bonds: A:Y.12, A:T.14, A:Y.46, A:S.53, A:Y.124, A:H.182, A:L.262 Water bridges: A:Y.12, A:R.45, A:Y.124, A:K.224 Salt bridges: A:R.45 pi-Stacking: A:H.182

1 x CA: CALCIUM ION(Non-functional Binders)

CA.7: 2 residues within 4Å: Chain A: S.221 Ligands: GOL.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dali, A. et al., Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation. Protein Sci. (2023)

Release Date

2022-12-28

Peptides

Ferrochelatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ferrochelatase

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