SMTL ID : 6t8z.1 (1 other biounit)

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A ternary complex with the oxidised form of the cofactor NAD+ and the substrate formate both at a primary and secondary sites.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

homo-dimer

Ligands

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 10 residues within 4Å: Chain A: Y.195, K.200, D.258, K.283, R.284, G.285, S.286, W.287, R.312 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.258, A:R.312 Water bridges: A:K.200, A:R.312 PEG.2: 9 residues within 4Å: Chain A: Y.108, L.109, T.110, D.131, H.132, V.133, D.134, R.271 Ligands: EDO.8 No protein-ligand interaction detected (PLIP) PEG.11: 9 residues within 4Å: Chain B: Y.195, K.200, D.258, K.283, R.284, G.285, S.286, W.287, R.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.312 Water bridges: B:K.200, B:K.283

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: Y.231, H.267, S.269, G.394, Q.395 Ligands: NAD.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.395, A:Q.395 FMT.4: 9 residues within 4Å: Chain A: P.103, F.104, G.127, I.128, N.154, R.293, H.346, G.349 Ligands: NAD.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.128, A:N.154, A:R.293, A:R.293, A:H.346 FMT.12: 6 residues within 4Å: Chain B: Y.231, H.267, S.269, G.394, Q.395 Ligands: NAD.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.395, B:Q.395 FMT.13: 9 residues within 4Å: Chain B: P.103, F.104, G.127, I.128, N.154, R.293, H.346, G.349 Ligands: NAD.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.128, B:N.154, B:R.293, B:R.293, B:H.346

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

NAD.5: 37 residues within 4Å: Chain A: F.104, I.128, G.129, N.154, V.155, V.158, V.205, G.206, V.207, G.208, R.209, I.210, G.211, Y.229, D.230, Y.231, Q.232, N.263, C.264, P.265, L.266, H.267, T.270, L.273, T.291, A.292, R.293, D.317, V.318, H.346, S.348, G.349, A.392, Y.393, G.394 Ligands: FMT.3, FMT.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.128, A:V.158, A:I.210 Hydrogen bonds: A:R.209, A:I.210, A:Y.231, A:Q.232, A:H.267, A:T.291, A:A.292, A:H.346, A:G.349, A:Y.393 Water bridges: A:D.131, A:G.208, A:R.209, A:R.209, A:G.211, A:Y.231, A:L.266, A:T.390 Salt bridges: A:R.209 NAD.14: 37 residues within 4Å: Chain B: F.104, I.128, G.129, N.154, V.155, V.158, V.205, G.206, V.207, G.208, R.209, I.210, G.211, Y.229, D.230, Y.231, Q.232, N.263, C.264, P.265, L.266, H.267, T.270, L.273, T.291, A.292, R.293, D.317, V.318, H.346, S.348, G.349, A.392, Y.393, G.394 Ligands: FMT.12, FMT.13 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.128, B:V.158, B:I.210 Hydrogen bonds: B:R.209, B:I.210, B:Y.231, B:Q.232, B:H.267, B:T.291, B:A.292, B:H.346, B:G.349, B:Y.393 Water bridges: B:D.131, B:G.208, B:R.209, B:R.209, B:G.211, B:L.266, B:T.390 Salt bridges: B:R.209

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

EDO.6: 7 residues within 4Å: Chain A: V.150, T.151, G.152, S.153, R.357, R.364, R.377 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.151, A:G.152, A:R.377, A:R.377 EDO.7: 7 residues within 4Å: Chain A: K.276, I.279, S.280, E.304, A.305, T.308, H.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.308 Water bridges: A:A.305 EDO.8: 10 residues within 4Å: Chain A: S.130, D.131, V.133, D.134, L.135, D.136, H.267, R.271, Y.388 Ligands: PEG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.131, A:D.134, A:D.134, A:L.135, A:D.136 Water bridges: A:R.271 EDO.9: 5 residues within 4Å: Chain A: V.201, K.224, D.258, K.283 Ligands: PEG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.224, A:D.258, A:K.283 Water bridges: A:V.201, A:V.201 EDO.10: 2 residues within 4Å: Chain A: D.44 Chain B: D.186 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.44 Hydrogen bonds: B:D.186 EDO.15: 8 residues within 4Å: Chain B: Y.108, L.109, T.110, D.131, H.132, V.133, D.134, R.271 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.134, B:L.135, B:L.135, B:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yilmazer, B. et al., Structural insights into the NAD + -dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD + ternary complex of the Chaetomium thermophilum enzyme. J.Struct.Biol. (2020)

Release Date

2020-11-18

Peptides

Formate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Formate dehydrogenase

Related Entries With Identical Sequence