SMTL ID : 6juj.1

Crystal structure of Formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F from Pseudomonas sp. 101in complex with non-natural cofactor Nicotinamide Cytosine Dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x A7R: [[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

A7R.1: 21 residues within 4Å: Chain A: F.99, N.147, V.151, A.199, G.201, R.202, I.203, D.222, R.223, N.255, I.256, P.257, H.259, T.283, A.284, R.285, D.309, V.310, H.333, S.335, G.336 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:R.202, A:I.203, A:D.222, A:R.223, A:H.259, A:A.284, A:A.284, A:D.309, A:G.336 Water bridges: A:G.201, A:R.202, A:R.202, A:G.204, A:N.381 A7R.5: 20 residues within 4Å: Chain B: F.99, N.147, V.151, A.199, G.201, R.202, I.203, D.222, R.223, N.255, I.256, P.257, H.259, T.283, A.284, D.309, V.310, H.333, S.335, G.336 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.151 Hydrogen bonds: B:R.202, B:I.203, B:D.222, B:R.223, B:H.259, B:D.309, B:G.336 Water bridges: B:G.201, B:R.202, B:R.202, B:G.204, B:R.242, B:R.242 Salt bridges: B:R.202 pi-Cation interactions: B:R.223

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: P.168, P.326, Y.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.327, A:Y.327 GOL.3: 5 residues within 4Å: Chain A: L.298, E.299, G.301, P.326, Y.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.299 Water bridges: A:G.301 GOL.4: 5 residues within 4Å: Chain A: G.124, S.125, D.126, E.142, N.381 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.125, A:D.126, A:D.126, A:E.142, A:N.381 GOL.6: 3 residues within 4Å: Chain B: R.360, P.361, R.363 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.360 GOL.7: 6 residues within 4Å: Chain B: Y.20, R.22, D.23, P.47, G.48, Q.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.48, B:Q.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, X. et al., Structure-Guided Design of Formate Dehydrogenase for Regeneration of a Non-Natural Redox Cofactor. Chemistry (2020)

Release Date

2020-05-13

Peptides

Formate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formate dehydrogenase

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