SMTL ID : 3n7u.1 (5 other biounits)

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: F.71, I.95, N.119, V.120, V.123, A.172, G.173, R.174, I.175, H.193, D.194, R.195, L.196, M.228, P.229, T.234, N.255, A.256, R.257, D.281, V.282, H.305, S.307, G.308, Q.349, Y.350 Ligands: AZI.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.95, A:V.123, A:I.175 Hydrogen bonds: A:A.172, A:R.174, A:I.175, A:R.195, A:N.255, A:G.308 Water bridges: A:G.173, A:R.174, A:R.174, A:G.176, A:R.195, A:L.230, A:T.231, A:Q.349, A:Y.350 Salt bridges: A:R.174 pi-Cation interactions: A:R.195 NAD.4: 27 residues within 4Å: Chain B: F.71, I.95, G.96, N.119, V.120, V.123, A.172, G.173, R.174, I.175, D.194, R.195, L.196, M.228, P.229, T.234, N.255, A.256, R.257, D.281, V.282, H.305, S.307, G.308, Q.349, Y.350 Ligands: AZI.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.95, B:V.123, B:I.175 Hydrogen bonds: B:R.174, B:I.175, B:R.195, B:D.281, B:G.308, B:Q.349 Water bridges: B:G.173, B:R.174, B:R.174, B:G.176, B:R.195, B:R.195, B:L.230, B:Y.350 Salt bridges: B:R.174 pi-Cation interactions: B:R.195

2 x AZI: AZIDE ION(Non-covalent)

AZI.2: 8 residues within 4Å: Chain A: P.70, F.71, G.94, I.95, N.119, R.257, H.305 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.95, A:N.119, A:R.257, A:R.257, A:H.305 AZI.5: 8 residues within 4Å: Chain B: P.70, F.71, G.94, I.95, N.119, R.257, H.305 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.95, B:N.119, B:R.257, B:R.257, B:H.305

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.327, P.335 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.327 SO4.6: 2 residues within 4Å: Chain B: R.327, P.335 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.336 Salt bridges: B:R.327

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain B: Y.157, R.158, N.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.158, B:N.299 Water bridges: B:V.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shabalin, I.G. et al., Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana. To be Published

Release Date

2010-06-09

Peptides

Formate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formate dehydrogenase

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