SMTL ID : 1hfe.3 (2 other biounits)

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.82, D.86 Chain C: H.82, D.86 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Metal complexes: A:D.86, C:H.82, C:D.86

4 x FE2: FE (II) ION(Non-covalent)(Non-functional Binders)

FE2.2: 7 residues within 4Å: Chain B: C.382 Ligands: FE2.3, CYN.4, CYN.5, PDT.9, CMO.10, CMO.11 3 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:C.382, H2O.6, CMO.10 FE2.3: 6 residues within 4Å: Ligands: FE2.2, CYN.4, CYN.5, PDT.9, CMO.10, CMO.11 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.6, CMO.11 FE2.13: 7 residues within 4Å: Chain D: C.382 Ligands: FE2.14, CYN.15, CYN.16, PDT.20, CMO.21, CMO.22 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.382, H2O.29 FE2.14: 6 residues within 4Å: Ligands: FE2.13, CYN.15, CYN.16, PDT.20, CMO.21, CMO.22 No protein-ligand interaction detected (PLIP)

4 x CYN: CYANIDE ION(Non-covalent)

CYN.4: 8 residues within 4Å: Chain B: S.202, P.203, I.204, K.237 Ligands: FE2.2, FE2.3, PDT.9, CMO.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.204 CYN.5: 9 residues within 4Å: Chain B: A.107, P.108, A.109, G.297, C.382 Ligands: FE2.2, FE2.3, PDT.9, CMO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.109 CYN.15: 8 residues within 4Å: Chain D: S.202, P.203, I.204, K.237 Ligands: FE2.13, FE2.14, PDT.20, CMO.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.204 CYN.16: 9 residues within 4Å: Chain D: A.107, P.108, A.109, G.297, C.382 Ligands: FE2.13, FE2.14, PDT.20, CMO.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.109

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.6: 13 residues within 4Å: Chain B: I.30, C.35, I.36, G.37, C.38, D.39, T.40, C.41, H.58, C.76, P.77, E.78, I.81 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:H.58 Metal complexes: B:C.35, B:C.38, B:C.41, B:C.76 SF4.7: 11 residues within 4Å: Chain B: C.45, P.46, T.47, I.50, I.60, C.66, I.67, N.68, C.69, G.70, C.72 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.45, B:C.66, B:C.69, B:C.72 SF4.8: 12 residues within 4Å: Chain B: C.179, P.180, P.233, C.234, K.237, M.376, A.377, C.378, C.382, G.385 Ligands: PDT.9, CMO.10 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.179, B:C.234, B:C.378, B:C.382 SF4.17: 13 residues within 4Å: Chain D: I.30, C.35, I.36, G.37, C.38, D.39, T.40, C.41, H.58, C.76, P.77, E.78, I.81 5 PLIP interactions: 5 interactions with chain D, pi-Cation interactions: D:H.58 Metal complexes: D:C.35, D:C.38, D:C.41, D:C.76 SF4.18: 11 residues within 4Å: Chain D: C.45, P.46, T.47, I.50, I.60, C.66, I.67, N.68, C.69, G.70, C.72 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.45, D:C.66, D:C.69, D:C.72 SF4.19: 11 residues within 4Å: Chain D: C.179, P.180, P.233, C.234, M.376, A.377, C.378, C.382, G.385 Ligands: PDT.20, CMO.21 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.179, D:C.234, D:C.378, D:C.382

2 x PDT: 1,3-PROPANEDITHIOL(Non-covalent)

PDT.9: 13 residues within 4Å: Chain B: C.178, C.179, K.237, F.296, M.376, C.382 Ligands: FE2.2, FE2.3, CYN.4, CYN.5, SF4.8, CMO.10, CMO.11 No protein-ligand interaction detected (PLIP) PDT.20: 13 residues within 4Å: Chain D: C.178, C.179, K.237, F.296, M.376, C.382 Ligands: FE2.13, FE2.14, CYN.15, CYN.16, SF4.19, CMO.21, CMO.22 No protein-ligand interaction detected (PLIP)

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.10: 10 residues within 4Å: Chain B: M.232, P.233, C.234, K.237, C.382 Ligands: FE2.2, FE2.3, CYN.5, SF4.8, PDT.9 No protein-ligand interaction detected (PLIP) CMO.11: 9 residues within 4Å: Chain B: P.108, T.145, A.149, P.203, F.296 Ligands: FE2.2, FE2.3, CYN.4, PDT.9 No protein-ligand interaction detected (PLIP) CMO.21: 10 residues within 4Å: Chain D: M.232, P.233, C.234, K.237, C.382 Ligands: FE2.13, FE2.14, CYN.16, SF4.19, PDT.20 No protein-ligand interaction detected (PLIP) CMO.22: 9 residues within 4Å: Chain D: P.108, T.145, A.149, P.203, F.296 Ligands: FE2.13, FE2.14, CYN.15, PDT.20 No protein-ligand interaction detected (PLIP)

2 x CYS: CYSTEINE(Non-covalent)

CYS.12: 12 residues within 4Å: Chain A: R.46 Chain B: Q.71, T.74, H.75, V.383, C.384, G.385, Q.388, P.389, V.390, M.391, V.394 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.71, B:T.74, B:T.74, B:P.389, B:M.391, A:R.46, A:R.46 Salt bridges: B:H.75, A:R.46 CYS.23: 12 residues within 4Å: Chain C: R.46 Chain D: Q.71, T.74, H.75, V.383, C.384, G.385, Q.388, P.389, V.390, M.391, V.394 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.71, D:T.74, D:P.389, D:M.391, C:R.46, C:R.46 Salt bridges: C:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, Y. et al., Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Structure Fold.Des. (1999)

Release Date

1999-04-20

Peptides

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)): AC
PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

B
L

D
M

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))

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