SMTL ID : 4kl8.1 (1 other biounit)

High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.207, H.208, C.211, Y.213, L.214, Y.217, C.231, K.232, A.233, C.237, G.239, P.240, V.259 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.208, A:C.211, A:C.231, A:C.237 SF4.2: 11 residues within 4Å: Chain A: T.242, C.246, W.251, C.258, C.264, I.265, G.266, C.267, V.268 Chain B: R.186, Q.191 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.246, A:C.258, A:C.264, A:C.267 SF4.3: 13 residues within 4Å: Chain A: G.17, C.18, G.20, C.21, E.77, G.124, T.125, C.126, G.163, C.164, P.165 Chain B: R.69, H.189 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.77 Metal complexes: A:C.18, A:C.21, A:C.126, A:C.164

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 1 residues within 4Å: Chain A: E.152 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.152, H2O.3, H2O.3, H2O.3, H2O.3 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 3 residues within 4Å: Chain B: E.52, I.445, H.499 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.52, B:I.445, B:H.499, H2O.15, H2O.15, H2O.15

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

CL.5: 5 residues within 4Å: Chain A: N.27, H.167, P.168, N.252, N.253 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: H.30, R.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.30, A:R.32, A:R.32 GOL.7: 3 residues within 4Å: Chain A: Y.62, D.112, K.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.112, A:K.116

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

FCO.9: 11 residues within 4Å: Chain B: C.74, H.78, A.424, P.425, R.426, L.429, A.448, T.449, U.493, C.496 Ligands: NI.10 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.426, B:R.426, B:A.448, B:T.449, B:T.449 Metal complexes: B:C.74, B:C.496, H2O.15

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

NI.10: 6 residues within 4Å: Chain B: C.71, V.73, C.74, U.493, C.496 Ligands: FCO.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.71, B:C.74, H2O.15

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.12: 6 residues within 4Å: Chain B: C.74, T.76, A.77, F.106, N.109, P.425 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase. Chem.Commun.(Camb.) (2013)

Release Date

2013-07-10

Peptides

Periplasmic [NiFeSe] hydrogenase small subunit: A
Nickel-dependent hydrogenase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
L

Periplasmic [NiFeSe] hydrogenase small subunit

Nickel-dependent hydrogenase large subunit

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