SMTL ID : 6juk.1

Crystal structure of Formate dehydrogenase mutant C256I/E261P/S381I from Pseudomonas sp. 101 in complex with non-natural cofactor Nicotinamide Cytosine Dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: H.30, G.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.33 GOL.2: 4 residues within 4Å: Chain A: Y.9, D.10, W.100 Chain B: W.178 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.178, A:D.10, A:D.10 Water bridges: B:N.179 GOL.3: 3 residues within 4Å: Chain A: T.74, S.75, D.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.74, A:S.75, A:D.76 Water bridges: A:V.73, A:T.74 GOL.4: 8 residues within 4Å: Chain A: Y.20, R.22, D.23, D.24, T.46, P.47, G.48, Q.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.22, A:P.47, A:Q.49 GOL.7: 4 residues within 4Å: Chain B: C.355, R.360, P.361, R.363 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.360 Water bridges: B:E.351, B:R.360 GOL.8: 1 residues within 4Å: Chain B: H.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.259, B:H.259

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.5: 21 residues within 4Å: Chain A: F.99, N.147, V.151, A.199, G.201, R.202, I.203, D.222, R.223, H.224, N.255, I.256, P.257, H.259, T.262, T.283, A.284, D.309, H.333, S.335, G.336 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.151, A:I.203 Hydrogen bonds: A:R.202, A:R.202, A:I.203, A:D.222, A:R.223, A:R.223, A:N.255, A:H.259, A:D.309, A:G.336 Water bridges: A:G.201, A:G.204, A:R.242, A:R.242, A:L.254, A:N.255 pi-Cation interactions: A:R.223 A7R.6: 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.262, T.283, A.284, D.309, H.333, S.335, G.336 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.151, B:I.203 Hydrogen bonds: B:R.202, B:I.203, B:D.222, B:R.223, B:N.255, B:H.259, B:D.309, B:G.336 Water bridges: B:G.201, B:G.204, B:R.242, B:T.283

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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