SMTL ID : 8bxx.1 (1 other biounit)

Crystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in complex with NAD and azide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 29 residues within 4Å: Chain A: F.99, I.123, G.124, N.147, S.148, V.151, V.198, A.199, G.201, R.202, I.203, F.221, D.222, Q.223, H.224, N.255, A.256, P.257, H.259, T.262, T.283, A.284, R.285, D.309, V.310, H.333, S.335, G.336 Ligands: AZI.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.123, A:V.151, A:I.203 Hydrogen bonds: A:R.202, A:I.203, A:Q.223, A:D.309, A:G.336 Water bridges: A:D.126, A:S.148, A:G.201, A:R.202, A:G.204, A:L.258 Salt bridges: A:R.202 NAD.4: 28 residues within 4Å: Chain B: F.99, I.123, N.147, S.148, V.151, V.198, A.199, G.201, R.202, I.203, F.221, D.222, Q.223, H.224, N.255, A.256, P.257, H.259, T.262, T.283, A.284, R.285, D.309, V.310, H.333, S.335, G.336 Ligands: AZI.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.123, B:V.151 Hydrogen bonds: B:R.202, B:I.203, B:Q.223, B:D.309, B:G.336 Water bridges: B:S.148, B:G.201, B:R.202, B:G.204, B:L.258, B:L.258 Salt bridges: B:R.202

2 x AZI: AZIDE ION(Non-covalent)

AZI.2: 8 residues within 4Å: Chain A: P.98, F.99, G.122, I.123, N.147, R.285, H.333 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.123, A:I.123, A:N.147, A:R.285, A:R.285 AZI.5: 8 residues within 4Å: Chain B: P.98, F.99, G.122, I.123, N.147, R.285, H.333 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.123, B:N.147, B:N.147, B:R.285, B:R.285, B:H.333

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: V.94, S.96, A.102, L.104, V.119, T.120, H.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.96, A:A.102, A:A.102, A:V.119 Water bridges: A:T.120 EDO.6: 9 residues within 4Å: Chain B: V.94, S.96, A.102, L.104, A.118, V.119, T.120, H.127, V.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.96, B:A.102, B:A.102, B:V.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rubini, R. et al., From the amelioration of a NADP+-dependent formate dehydrogenase to the discovery of a new enzyme: round trip from theory to practice. ChemCatChem (2020)

Release Date

2023-01-18

Peptides

Formate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
DD

Formate dehydrogenase

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