SMTL ID : 3hcp.1

Human ferrochelatase with Mn and deuteroporphyrin bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 6 residues within 4Å: Chain A: C.132, R.208, S.338, C.339, C.342, C.347 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.132, A:C.339, A:C.342, A:C.347 FES.7: 6 residues within 4Å: Chain B: C.132, R.208, S.338, C.339, C.342, C.347 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.132, B:C.339, B:C.342, B:C.347

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.2: 12 residues within 4Å: Chain A: F.29, L.37, R.50, R.51, P.202, S.204, V.241, G.242, P.243, M.244, W.246 Ligands: FDE.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.29, A:L.37, A:P.202, A:P.202, A:M.244, A:W.246 Hydrogen bonds: A:S.204, A:V.241 Water bridges: A:S.204, A:S.204 Salt bridges: A:R.50, A:R.51 CHD.3: 9 residues within 4Å: Chain A: E.16, I.62, G.63, G.64, G.65, S.66, P.67, I.70, L.281 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.70 Hydrogen bonds: A:G.63 Water bridges: A:D.276, A:D.276 CHD.8: 13 residues within 4Å: Chain B: F.29, M.35, L.37, I.47, R.50, R.51, P.202, S.204, V.241, G.242, M.244, W.246 Ligands: FDE.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.29, B:M.35, B:I.47, B:P.202, B:P.202, B:M.244, B:W.246 Hydrogen bonds: B:S.204, B:V.241 Water bridges: B:S.204, B:S.204 Salt bridges: B:R.50, B:R.51 CHD.9: 8 residues within 4Å: Chain B: E.16, I.62, G.63, G.64, G.65, S.66, P.67, L.281 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.67 Hydrogen bonds: B:G.63 Water bridges: B:D.276, B:D.276

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: P.213, Q.214, S.217, W.237 Chain B: P.213, Q.214, S.217, W.237 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.237, B:S.217, B:S.217 Water bridges: A:Q.214

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 6 residues within 4Å: Chain A: H.199, S.200, Q.238, S.239, W.246 Ligands: FDE.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.239 pi-Stacking: A:H.199 IMD.10: 6 residues within 4Å: Chain B: H.199, S.200, Q.238, S.239, W.246 Ligands: FDE.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.239, B:S.239 pi-Stacking: B:H.199

2 x FDE: FE(III) DEUTEROPORPHYRIN IX(Non-covalent)

FDE.6: 22 residues within 4Å: Chain A: M.12, P.15, F.24, L.28, F.29, L.34, M.35, R.51, I.55, Y.59, S.133, T.134, H.199, L.201, P.202, Y.212, V.241, F.273, I.278, E.279 Ligands: CHD.2, IMD.5 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.24, A:L.28, A:F.29, A:L.34, A:T.134, A:H.199, A:P.202, A:Y.212, A:I.278, A:E.279 Hydrogen bonds: A:Y.59 Water bridges: A:Q.58, A:I.278, A:E.279 Salt bridges: A:R.51 pi-Stacking: A:H.199, A:W.246 FDE.11: 21 residues within 4Å: Chain B: M.12, P.15, F.24, F.29, L.34, M.35, R.51, I.55, Y.59, S.133, T.134, H.199, L.201, P.202, Y.212, V.241, H.277, I.278, E.279 Ligands: CHD.8, IMD.10 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:F.24, B:F.29, B:L.34, B:T.134, B:H.199, B:P.202, B:Y.212, B:I.278 Hydrogen bonds: B:Y.59 Water bridges: B:I.278, B:E.279 Salt bridges: B:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medlock, A.E. et al., Product release rather than chelation determines metal specificity for ferrochelatase. J.Mol.Biol. (2009)

Release Date

2009-11-10

Peptides

Ferrochelatase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ferrochelatase, mitochondrial

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