SMTL ID : 3vth.2 (1 other biounit)

Crystal structure of full-length HypF in the phosphate- and nucleotide-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: K.588 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.588

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.114, C.117, C.136, C.139 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.114, A:C.117, A:C.136, A:C.139

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 1 residues within 4Å: Chain A: Y.151 No protein-ligand interaction detected (PLIP) PO4.8: 3 residues within 4Å: Chain A: K.528, G.751, S.752 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.752 Salt bridges: A:K.528

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.4: 19 residues within 4Å: Chain A: K.245, R.247, K.250, P.251, F.252, A.253, L.285, T.303, L.304, G.305, T.328, S.329, N.331, S.333, E.334, V.370, R.382, M.622 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.247, A:R.247, A:K.250, A:K.250, A:T.303, A:T.303, A:G.305, A:S.329, A:S.329, A:E.334, A:R.382, A:R.382 Salt bridges: A:K.245

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: S.329, D.367, R.382 Ligands: APC.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.329

1 x AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

AP2.6: 20 residues within 4Å: Chain A: Y.409, H.483, H.487, D.507, G.508, T.509, G.598, R.599, F.601, E.617, G.618, A.621, E.625, G.702, S.703, Q.705, N.706, N.733, D.734 Ligands: FE.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.508, A:T.509, A:T.509, A:T.509, A:R.599, A:E.617, A:E.625, A:E.625, A:G.702, A:N.706, A:D.734 Water bridges: A:Y.409, A:R.707 pi-Stacking: A:F.601

1 x FE: FE (III) ION(Non-covalent)

FE.7: 5 residues within 4Å: Chain A: H.483, H.487, D.507, D.734 Ligands: AP2.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.483, A:H.487, A:D.507, A:D.734

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shomura, Y. et al., Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases. J.Biol.Chem. (2012)

Release Date

2012-07-04

Peptides

Hydrogenase maturation factor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hydrogenase maturation factor

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