SMTL ID : 3ze8.1

3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the reduced state at 1.95 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.208, C.211, Y.213, L.214, Y.217, C.232, R.233, Y.234, C.238, G.240, P.241, V.260 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.208, A:C.211, A:C.232, A:C.238 SF4.2: 11 residues within 4Å: Chain A: T.243, A.245, C.247, W.252, C.259, C.265, I.266, G.267, C.268 Chain B: R.171, Q.176 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.247, A:C.259, A:C.265, A:C.268 SF4.3: 13 residues within 4Å: Chain A: G.17, C.18, G.20, C.21, E.77, G.119, T.120, C.121, G.158, C.159, P.160 Chain B: R.62, H.174 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.77 Metal complexes: A:C.18, A:C.21, A:C.121, A:C.159

5 x C15: N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE(Non-covalent)

C15.4: 9 residues within 4Å: Chain A: S.22, L.25, L.26, I.33, L.37, L.43, H.46 Chain B: E.156 Ligands: C15.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.25, A:L.26, A:L.26, A:I.33, A:L.37, A:L.43 C15.5: 3 residues within 4Å: Chain B: Y.151 Ligands: C15.4, C15.11 No protein-ligand interaction detected (PLIP) C15.6: 7 residues within 4Å: Chain A: P.8, V.10, I.41, F.73, V.170, L.174, I.177 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.8, A:V.10, A:I.41, A:F.73, A:F.73, A:F.73, A:V.170, A:L.174, A:I.177, A:I.177 C15.11: 8 residues within 4Å: Chain B: Q.117, V.120, G.122, P.123, F.128, V.148, Y.151 Ligands: C15.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.117, B:V.120, B:P.123, B:F.128, B:F.128, B:F.128, B:V.148, B:Y.151, B:Y.151, B:Y.151 C15.12: 7 residues within 4Å: Chain B: F.225, K.226, L.338, F.342, I.344, L.352, A.356 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.225, B:F.225, B:K.226, B:L.338, B:F.342, B:L.352, B:A.356

1 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.7: 11 residues within 4Å: Chain B: C.67, H.71, A.409, P.410, R.411, L.414, A.433, S.434, U.478, C.481 Ligands: NI.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.411, B:R.411, B:A.433, B:S.434 Metal complexes: B:C.67, B:C.481

1 x NI: NICKEL (II) ION(Non-covalent)

NI.8: 5 residues within 4Å: Chain B: C.64, C.67, U.478, C.481 Ligands: FCO.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.67, B:C.481

1 x FE2: FE (II) ION(Non-covalent)

FE2.9: 3 residues within 4Å: Chain B: E.45, I.430, H.484 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.45, B:I.430, B:H.484, H2O.12, H2O.12, H2O.20

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

CL.10: 6 residues within 4Å: Chain B: C.67, T.69, A.70, F.99, N.102, P.410 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marques, M.C. et al., Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough. Int.J.Hydrogen Energy (2013)

Release Date

2013-06-12

Peptides

PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT: A
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT

PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING

Related Entries With Identical Sequence