SMTL ID : 1e3d.2 (1 other biounit)

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.1: 14 residues within 4Å: Chain A: V.186, T.226, N.228, C.230, F.235, W.240, P.241, C.248, I.249, G.250, C.251, S.252 Chain B: K.222, Q.227 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.230, A:C.248, A:C.251

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

SF4.2: 14 residues within 4Å: Chain A: V.186, H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, W.240, V.242 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221

1 x FSX: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)(Covalent)

FSX.3: 17 residues within 4Å: Chain A: E.16, C.17, T.18, G.19, C.20, E.75, G.76, G.112, T.113, C.114, I.120, G.149, C.150, P.151, P.152 Chain B: R.69, H.225 10 PLIP interactions: 10 interactions with chain A, Hydrogen bonds: A:C.17, A:T.18, A:G.19, A:C.20 Water bridges: A:G.76 Metal complexes: A:C.17, A:C.20, A:E.75, A:C.114, A:C.150

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 7 residues within 4Å: Chain A: T.113, Y.117, G.119, P.254, N.255, F.256, W.257 No protein-ligand interaction detected (PLIP) H2S.7: 6 residues within 4Å: Chain B: T.77, L.106, Q.109, F.110, V.467, S.468 No protein-ligand interaction detected (PLIP)

1 x FNE: (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)(Non-covalent)

FNE.5: 14 residues within 4Å: Chain B: C.71, V.73, C.74, T.77, H.78, V.467, S.468, R.469, L.472, V.490, P.491, T.492, C.536, C.539 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.469, B:R.469, B:T.492, B:T.492 Metal complexes: B:C.71, B:C.74, B:C.74, B:C.536, B:C.539, B:C.539

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: E.52, K.365, L.488, H.542 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.52, B:L.488, B:H.542, H2O.11, H2O.21, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matias, P.M. et al., [Nife] Hydrogenase from Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of its Interaction with the Tetrahaem Cytochrome C3. J.Biol.Inorg.Chem. (2001)

Release Date

2001-06-14

Peptides

[NiFe] hydrogenase small subunit: A
[NiFe] hydrogenase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

[NiFe] hydrogenase small subunit

[NiFe] hydrogenase large subunit

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