SMTL ID : 4njo.1

crystal structure of cofactor(NAD+) bound 3-phosphoglycerate dehydrogenase in Entamoeba histolytica

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: A.80, N.104, V.108, G.141, C.142, G.143, Y.144, V.145, Y.163, D.164, P.165, F.166, H.189, L.190, P.191, E.195, T.196, T.217, A.218, R.219, D.243, K.265, G.267, A.268 Ligands: FMT.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.108 Hydrogen bonds: A:C.142, A:Y.144, A:V.145, A:D.243, A:K.265, A:A.268 Water bridges: A:D.83, A:G.102, A:L.192, A:E.269

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

FMT.2: 7 residues within 4Å: Chain A: R.77, A.80, G.81, N.104, R.219, K.265 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.77, A:A.80, A:G.81, A:R.219, A:R.219, A:K.265, A:K.265 FMT.3: 7 residues within 4Å: Chain B: R.77, G.79, A.80, G.81, N.104, R.219 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.80, B:G.81, B:N.104, B:R.219, B:R.219 Water bridges: B:R.219

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain B: A.80, G.141, G.143, Y.144, V.145, G.146, H.189 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.141, B:G.143, B:V.145, B:G.146, B:H.189

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain B: K.11, R.57, S.58, R.77, A.78, K.265, A.268 Ligands: FMT.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.11, B:K.11, B:R.57, B:R.77, B:R.77, B:A.78, B:N.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.K. et al., Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine. Febs J. (2014)

Release Date

2014-10-08

Peptides

D-3-phosphoglycerate dehydrogenase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-3-phosphoglycerate dehydrogenase, putative

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