SMTL ID : 6t94.2 (1 other biounit)

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein with the reduced form of the cofactor NADH.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 9 residues within 4Å: Chain A: Y.195, K.200, D.258, K.283, R.284, G.285, S.286, W.287, R.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.258, A:R.312 Water bridges: A:K.283, A:R.284 PEG.4: 9 residues within 4Å: Chain B: Y.195, K.200, D.258, K.283, R.284, G.285, S.286, W.287, R.312 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.195 Water bridges: B:K.283 PEG.5: 10 residues within 4Å: Chain B: Y.108, L.109, T.110, A.111, D.131, H.132, V.133, D.134, L.135, R.271 No protein-ligand interaction detected (PLIP)

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 36 residues within 4Å: Chain A: F.104, I.128, G.129, C.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, R.391, A.392, Y.393, G.394 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.128, A:V.158, A:I.210 Hydrogen bonds: A:R.209, A:I.210, A:D.230, A:Q.232, A:H.267, A:T.291, A:H.346, A:G.349, A:Y.393 Water bridges: A:G.129, A:G.208, A:R.209, A:R.209, A:G.211, A:L.266, A:L.266, A:T.390 Salt bridges: A:R.209 NAI.6: 36 residues within 4Å: Chain B: F.104, I.128, G.129, C.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, R.391, A.392, Y.393, G.394 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:D.230, B:Q.232, B:H.267, B:T.291, B:H.346, B:G.349, B:Y.393 Water bridges: B:G.208, B:R.209, B:R.209, B:G.211, B:L.266, B:L.266, B:R.293, B:T.390 Salt bridges: B:R.209

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

EDO.3: 2 residues within 4Å: Chain A: E.252, A.255 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.251, A:E.252 EDO.7: 2 residues within 4Å: Chain B: R.307, P.336 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.336 Water bridges: B:R.307, B:R.307 EDO.8: 7 residues within 4Å: Chain B: K.276, I.279, S.280, E.304, A.305, T.308, H.310 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.276 Water bridges: B:A.305

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
CCC

B
DDD

Formate dehydrogenase

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