SMTL ID : 2qd5.1

Structure of wild type human ferrochelatase in complex with a lead-porphyrin compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PB: LEAD (II) ION(Non-functional Binders)

PB.1: 3 residues within 4Å: Ligands: PP9.5, ACY.7, ACY.8 No protein-ligand interaction detected (PLIP) PB.9: 2 residues within 4Å: Ligands: PP9.13, ACY.15 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: ACY.15

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

FES.2: 5 residues within 4Å: Chain A: C.132, 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.10: 5 residues within 4Å: Chain B: C.132, 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.3: 11 residues within 4Å: Chain A: M.35, T.36, L.37, R.51, P.202, S.204, V.241, G.242, M.244 Ligands: CHD.4, PP9.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.35, A:L.37, A:P.202, A:V.241 Hydrogen bonds: A:S.204, A:S.204, A:G.242 Water bridges: A:R.51, A:S.204 Salt bridges: A:R.51, A:K.54 CHD.4: 4 residues within 4Å: Chain A: L.37, P.38, R.50 Ligands: CHD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.37 Hydrogen bonds: A:R.50, A:R.50 CHD.11: 11 residues within 4Å: Chain B: M.35, T.36, L.37, R.50, P.202, S.204, V.241, G.242, M.244 Ligands: CHD.12, PP9.13 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.35, B:L.37, B:P.202, B:P.202, B:V.241 Hydrogen bonds: B:S.204, B:S.204 Water bridges: B:M.244 Salt bridges: B:R.50, B:R.51 CHD.12: 4 residues within 4Å: Chain B: L.37, P.38, L.43 Ligands: CHD.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.37, B:P.38, B:L.43

2 x PP9: PROTOPORPHYRIN IX(Non-covalent)

PP9.5: 25 residues within 4Å: Chain A: M.12, L.28, F.29, L.34, R.51, I.55, Y.59, S.131, 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: PB.1, CHD.3, ACY.7, ACY.8 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.28, A:L.28, A:F.29, A:L.34, A:I.55, A:T.134, A:H.199, A:V.205, A:Y.212, A:F.273, A:F.273, A:I.278 Hydrogen bonds: A:I.278 Water bridges: A:S.239 Salt bridges: A:R.51, A:H.199 pi-Stacking: A:W.246 PP9.13: 26 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, Y.212, S.239, V.241, W.246, A.272, F.273, H.277, I.278 Ligands: PB.9, CHD.11, OXY.14, ACY.15 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:Y.212, B:W.246, B:F.273, B:F.273, B:I.278 Hydrogen bonds: B:S.239, B:I.278 Salt bridges: B:R.51, B:H.199 pi-Stacking: B:W.246

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: P.213, S.217, W.237 Chain B: P.213, S.217, W.237, L.247 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.217, B:S.217, A:S.217 Water bridges: B:W.237, A:W.237

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 8 residues within 4Å: Chain A: M.12, L.34, Y.101, Y.127, S.133, T.134 Ligands: PB.1, PP9.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.34, A:Y.101 Hydrogen bonds: A:Y.127, A:Y.127 ACY.8: 7 residues within 4Å: Chain A: H.199, S.200, S.239, K.240, W.246 Ligands: PB.1, PP9.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.200, A:K.240 Salt bridges: A:H.199 ACY.15: 9 residues within 4Å: Chain B: H.199, S.200, Q.238, S.239, K.240, V.241, W.246 Ligands: PB.9, PP9.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.246 Hydrogen bonds: B:S.239, B:K.240 Salt bridges: B:H.199

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.14: 3 residues within 4Å: Chain B: S.133, T.134 Ligands: PP9.13 No protein-ligand interaction detected (PLIP)

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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