SMTL ID : 4klr.1

E343Q variant of human ferrochelatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 6 residues within 4Å: Chain A: H.210, S.211, Q.249, S.250, W.257 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.210 IMD.9: 7 residues within 4Å: Chain B: H.210, S.211, Q.249, S.250, K.251, W.257 Ligands: HEM.14 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:H.210

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

BCT.2: 6 residues within 4Å: Chain A: M.23, L.45, Y.112, S.144, T.145 Ligands: HEM.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.138 Water bridges: A:D.42 BCT.10: 6 residues within 4Å: Chain B: M.23, L.45, Y.112, S.144, T.145 Ligands: HEM.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.138

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.224, Q.225, S.228, L.258 Chain B: P.224, S.228, W.248 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.228, B:S.228 Water bridges: A:Q.225, A:W.248, B:W.248

5 x CHD: CHOLIC ACID(Non-covalent)(Covalent)

CHD.4: 11 residues within 4Å: Chain A: T.47, L.48, R.61, R.62, P.213, S.215, V.252, G.253, M.255 Ligands: CHD.5, HEM.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.48, A:P.213, A:P.213, A:V.252, A:M.255 Hydrogen bonds: A:S.215, A:S.215, A:V.252 Salt bridges: A:R.61, A:R.62 CHD.5: 6 residues within 4Å: Chain A: L.48, P.49, L.54, I.58, R.61 Ligands: CHD.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.48, A:L.54, A:I.58 Hydrogen bonds: A:T.47 CHD.11: 12 residues within 4Å: Chain B: F.40, T.47, L.48, R.62, P.213, S.215, K.251, V.252, G.253, M.255 Ligands: CHD.12, HEM.14 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.40, B:L.48, B:P.213, B:P.213, B:K.251, B:M.255 Hydrogen bonds: B:S.215, B:S.215, B:G.253 Salt bridges: B:R.62 CHD.12: 4 residues within 4Å: Chain B: L.48, P.49, R.61 Ligands: CHD.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.48, B:P.49 CHD.13: 3 residues within 4Å: Chain A: E.239, Y.240 Chain B: E.340 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.240 Hydrogen bonds: A:E.239 Water bridges: A:Q.232

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: K.167, W.168, L.341, Q.369 Ligand excluded by PLIP

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

HEM.7: 23 residues within 4Å: Chain A: M.23, L.36, L.39, F.40, L.45, R.62, I.66, Y.70, S.144, T.145, H.210, L.212, P.213, Y.223, V.252, W.257, A.283, F.284, H.288, I.289 Ligands: IMD.1, BCT.2, CHD.4 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.36, A:L.39, A:L.39, A:F.40, A:L.45, A:T.145, A:H.210, A:Y.223, A:V.252, A:F.284, A:F.284, A:I.289 Hydrogen bonds: A:Y.70, A:I.289 Salt bridges: A:R.62, A:H.210 pi-Stacking: A:W.257 HEM.14: 23 residues within 4Å: Chain B: M.23, L.36, L.39, F.40, L.45, R.62, I.66, Y.70, Y.138, S.144, T.145, H.210, L.212, P.213, Y.223, W.257, A.283, F.284, H.288, I.289 Ligands: IMD.9, BCT.10, CHD.11 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.36, B:L.39, B:L.39, B:F.40, B:L.45, B:Y.138, B:T.145, B:H.210, B:Y.223, B:W.257, B:F.284, B:I.289 Hydrogen bonds: B:Y.70, B:I.289 Salt bridges: B:R.62, B:H.210, B:K.251 pi-Stacking: B:W.257 pi-Cation interactions: B:K.251

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

FES.8: 6 residues within 4Å: Chain A: C.143, R.219, S.349, C.350, C.353, C.358 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.143, A:C.350, A:C.353, A:C.358 FES.15: 6 residues within 4Å: Chain B: C.143, R.219, S.349, C.350, C.353, C.358 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.143, B:C.350, B:C.353, B:C.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lanzilotta, W.N. et al., E343Q variant of human ferrochelatase. To be Published

Release Date

2014-06-18

Peptides

Ferrochelatase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ferrochelatase, mitochondrial