SMTL ID : 6d4c.1

Crystal structure of Candida boidinii formate dehydrogenase V123G mutant complexed with NAD+ and azide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 38 residues within 4Å: Chain A: F.69, V.93, G.94, D.96, N.119, V.120, I.170, G.171, A.172, G.173, R.174, I.175, G.176, Y.194, D.195, Y.196, Q.197, N.228, A.229, P.230, L.231, H.232, G.234, T.235, L.238, T.256, A.257, R.258, D.282, V.283, H.311, S.313, G.314, A.357, Y.358, G.359 Ligands: AZI.2, CL.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.93, A:I.175 Hydrogen bonds: A:G.173, A:R.174, A:I.175, A:Y.196, A:H.232, A:G.234, A:T.256, A:H.311, A:S.313, A:G.314, A:Y.358, A:Y.358 Water bridges: A:G.94, A:D.96, A:R.174, A:R.174, A:G.176, A:Y.194, A:Y.194, A:Y.196, A:Y.196, A:L.231 Salt bridges: A:R.174 NAD.4: 38 residues within 4Å: Chain B: F.69, V.93, G.94, D.96, N.119, V.120, I.170, G.171, A.172, G.173, R.174, I.175, G.176, Y.194, D.195, Y.196, Q.197, N.228, A.229, P.230, L.231, H.232, G.234, T.235, L.238, T.256, A.257, R.258, D.282, V.283, H.311, S.313, G.314, A.357, Y.358, G.359 Ligands: AZI.5, CL.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:V.93, B:I.175 Hydrogen bonds: B:G.173, B:R.174, B:I.175, B:H.232, B:T.256, B:H.311, B:S.313, B:G.314, B:Y.358, B:Y.358 Water bridges: B:G.94, B:D.96, B:R.174, B:R.174, B:G.176, B:Y.194, B:Y.196, B:Y.196, B:Y.196, B:L.231 Salt bridges: B:R.174

2 x AZI: AZIDE ION(Non-covalent)

AZI.2: 9 residues within 4Å: Chain A: P.68, F.69, G.92, V.93, N.119, R.258, H.311, G.314 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.93, A:V.93, A:N.119, A:R.258, A:R.258, A:H.311 AZI.5: 9 residues within 4Å: Chain B: P.68, F.69, G.92, V.93, N.119, R.258, H.311, G.314 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.93, B:N.119, B:R.258, B:R.258, B:H.311

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

CL.3: 5 residues within 4Å: Chain A: Y.196, H.232, G.234, G.359 Ligands: NAD.1 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: Y.196, H.232, G.234, G.359 Ligands: NAD.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pagano, P.L. et al., Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase. Acs Catalysis (2019)

Release Date

2019-04-24

Peptides

Formate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formate dehydrogenase