SMTL ID : 3hco.1

Human ferrochelatase with Cd and protoporphyrin IX bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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.8: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: P.213, Q.214, S.217, W.237 Chain B: P.213, S.217, L.235, W.237 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:W.237, B:S.217, B:S.217 Water bridges: A:Q.214, B:W.237

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 6 residues within 4Å: Chain A: H.199, S.200, Q.238, S.239, W.246 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.199 IMD.9: 6 residues within 4Å: Chain B: H.199, S.200, S.239, W.246 Ligands: IMD.10, HEM.14 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:H.199 IMD.10: 7 residues within 4Å: Chain B: M.12, L.34, Y.101, S.133, T.134 Ligands: IMD.9, HEM.14 No protein-ligand interaction detected (PLIP)

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.4: 7 residues within 4Å: Chain A: M.12, L.34, Y.101, Y.127, S.133, T.134 Ligands: HEM.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101, A:Y.127

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.5: 5 residues within 4Å: Chain A: L.37, P.38, L.43, R.50 Ligands: CHD.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.37, A:P.38, A:L.43 Hydrogen bonds: A:R.50 CHD.6: 13 residues within 4Å: Chain A: F.29, M.35, T.36, L.37, R.51, P.202, S.204, V.241, G.242, P.243, M.244 Ligands: CHD.5, HEM.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.37, A:P.202, A:P.202, A:V.241 Hydrogen bonds: A:S.204, A:S.204 Water bridges: A:M.244 Salt bridges: A:R.51 CHD.11: 6 residues within 4Å: Chain B: L.37, P.38, L.43, F.46, R.50 Ligands: CHD.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.37, B:L.43, B:F.46 Hydrogen bonds: B:R.50 CHD.12: 13 residues within 4Å: Chain B: M.35, T.36, L.37, R.50, R.51, P.202, S.204, V.241, G.242, P.243, M.244 Ligands: CHD.11, HEM.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.37, B:P.202, B:P.202, B:V.241, B:M.244 Salt bridges: B:R.50, B:R.51

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.7: 25 residues within 4Å: Chain A: M.12, L.25, L.28, F.29, L.34, R.51, I.55, Y.59, Y.127, S.133, T.134, H.199, L.201, P.202, V.205, Y.212, V.241, W.246, A.272, F.273, H.277, I.278 Ligands: IMD.3, BCT.4, CHD.6 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.25, A:L.28, A:L.28, A:F.29, A:L.34, A:Y.127, A:T.134, A:H.199, A:V.205, A:V.241, A:W.246, A:F.273, A:I.278 Hydrogen bonds: A:I.278 Salt bridges: A:R.51, A:H.199 pi-Stacking: A:W.246 HEM.14: 25 residues within 4Å: Chain B: M.12, L.25, L.28, F.29, L.34, R.51, I.55, Y.59, Y.127, S.133, T.134, H.199, L.201, P.202, V.205, Y.212, V.241, W.246, A.272, F.273, H.277, I.278 Ligands: IMD.9, IMD.10, CHD.12 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.25, B:L.28, B:L.28, B:F.29, B:L.34, B:I.55, B:Y.127, B:T.134, B:H.199, B:P.202, B:V.205, B:W.246, B:F.273, B:I.278 Hydrogen bonds: B:I.278 Water bridges: B:Y.59 Salt bridges: B:R.51, B:H.199 pi-Stacking: B:W.246

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 3 residues within 4Å: Chain B: R.51, V.241, G.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.242 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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