SMTL ID : 2qd2.1

F110A variant of human ferrochelatase with protoheme bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

BCT.1: 6 residues within 4Å: Chain A: M.12, L.34, Y.101, S.133, T.134 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) BCT.8: 7 residues within 4Å: Chain B: M.12, L.34, Y.101, Y.127, S.133, T.134 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.127

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

FES.2: 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.9: 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

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.239 Water bridges: A:S.239 pi-Stacking: A:H.199 IMD.4: 6 residues within 4Å: Chain A: P.213, S.217, L.247 Chain B: P.213, S.217, L.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.217, A:S.217 IMD.10: 7 residues within 4Å: Chain B: H.199, S.200, Q.238, S.239, K.240, W.246 Ligands: HEM.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.239 pi-Stacking: B:H.199

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.5: 11 residues within 4Å: Chain A: M.35, T.36, L.37, R.50, R.51, P.202, S.204, V.241, M.244 Ligands: CHD.6, HEM.7 10 PLIP interactions: 10 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:V.241, A:W.246 Salt bridges: A:R.50, A:R.51 CHD.6: 5 residues within 4Å: Chain A: L.37, P.38, L.43, R.50 Ligands: CHD.5 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.11: 12 residues within 4Å: Chain B: M.35, L.37, R.51, K.54, P.202, S.204, V.241, G.242, M.244, W.246 Ligands: CHD.12, HEM.13 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.37, B:P.202, B:P.202, B:V.241, B:W.246 Hydrogen bonds: B:S.204, B:S.204 Water bridges: B:M.244, B:W.246 Salt bridges: B:R.51, B:K.54 CHD.12: 3 residues within 4Å: Chain B: L.37, P.38 Ligands: CHD.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.37, B:P.38

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

HEM.7: 25 residues within 4Å: Chain A: M.12, L.28, F.29, L.34, R.51, I.55, Y.59, Y.127, S.133, T.134, H.199, S.200, L.201, P.202, V.205, Y.212, V.241, W.246, A.272, F.273, H.277, I.278 Ligands: BCT.1, IMD.3, CHD.5 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: 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:Y.212, A:W.246, A:F.273, A:F.273, A:I.278 Hydrogen bonds: A:I.278 Water bridges: A:Y.59, A:S.239 Salt bridges: A:R.51, A:K.54, A:H.199 pi-Stacking: A:H.199 HEM.13: 26 residues within 4Å: Chain B: M.12, L.25, L.28, F.29, L.34, M.35, 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: BCT.8, IMD.10, CHD.11 21 PLIP interactions: 21 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:Y.212, B:W.246, B:F.273, B:F.273, B:I.278 Hydrogen bonds: B:I.278 Water bridges: B:S.239 Salt bridges: B:R.51, B:K.54, B:H.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medlock, A.E. et al., A pi-Helix Switch Selective for Porphyrin Deprotonation and Product Release in Human Ferrochelatase. J.Mol.Biol. (2007)

Release Date

2007-10-30

Peptides

Ferrochelatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ferrochelatase

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