SMTL ID : 8hrq.1

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K) in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x CS: CESIUM ION(Non-covalent)

CS.1: 6 residues within 4Å: Chain A: D.35, K.37, N.39, V.75, Y.76, A.77 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.37 CS.7: 4 residues within 4Å: Chain B: P.142, E.143, N.146, E.336 No protein-ligand interaction detected (PLIP) CS.11: 6 residues within 4Å: Chain C: D.35, K.37, N.39, V.75, Y.76, A.77 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:K.37 CS.17: 4 residues within 4Å: Chain D: P.142, E.143, N.146, E.336 No protein-ligand interaction detected (PLIP)

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

NAD.2: 22 residues within 4Å: Chain A: G.9, F.10, G.11, R.12, I.13, N.34, D.35, S.36, K.37, E.78, R.79, S.97, T.98, G.99, F.100, S.121, A.122, C.153, T.183, N.315, E.316, Y.319 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.319 Hydrogen bonds: A:F.10, A:R.12, A:I.13, A:N.34, A:S.36, A:R.79, A:N.315 Water bridges: A:G.99, A:S.121, A:G.184 NAD.8: 21 residues within 4Å: Chain B: G.9, F.10, G.11, R.12, I.13, D.35, S.36, K.37, E.78, R.79, S.97, T.98, G.99, F.100, F.101, S.121, A.122, C.153, T.183, N.315, Y.319 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.319 Hydrogen bonds: B:F.10, B:F.10, B:R.12, B:I.13, B:S.36, B:R.79, B:N.315 Water bridges: B:G.11, B:G.14, B:R.15, B:R.15, B:G.184, B:G.184 NAD.12: 22 residues within 4Å: Chain C: G.9, F.10, G.11, R.12, I.13, N.34, D.35, S.36, K.37, E.78, R.79, S.97, T.98, G.99, F.100, S.121, A.122, C.153, T.183, N.315, E.316, Y.319 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.319 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.34, C:S.36, C:R.79, C:N.315, C:E.316 Water bridges: C:G.99, C:S.121, C:G.184 NAD.18: 21 residues within 4Å: Chain D: G.9, F.10, G.11, R.12, I.13, D.35, S.36, K.37, E.78, R.79, S.97, T.98, G.99, F.100, F.101, S.121, A.122, C.153, T.183, N.315, Y.319 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.13, D:Y.319 Hydrogen bonds: D:F.10, D:F.10, D:R.12, D:I.13, D:S.36, D:R.79, D:N.315 Water bridges: D:G.11, D:G.14, D:R.15, D:R.15, D:G.184, D:G.184, D:E.316

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

EDO.3: 4 residues within 4Å: Chain A: V.21, L.22, E.23, S.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.21 EDO.4: 5 residues within 4Å: Chain A: R.197, Y.231 Chain D: G.298, L.299, K.301 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Water bridges: A:D.195, A:S.210 Hydrogen bonds: D:K.301, D:K.301 EDO.13: 4 residues within 4Å: Chain C: V.21, L.22, E.23, S.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.21 EDO.14: 5 residues within 4Å: Chain B: G.298, L.299, K.301 Chain C: R.197, Y.231 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.301, B:K.301 Water bridges: C:D.195, C:S.210

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.60, Y.61, D.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.61 GOL.9: 3 residues within 4Å: Chain B: N.166, D.167, G.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.167 GOL.15: 3 residues within 4Å: Chain C: E.60, Y.61, D.62 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.61 GOL.19: 3 residues within 4Å: Chain D: N.166, D.167, G.170 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.167

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 6 residues within 4Å: Chain A: T.284, V.287 Chain B: D.49, S.50, I.51, G.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.284 PO4.10: 5 residues within 4Å: Chain A: S.50, I.51, G.53 Chain B: T.284, V.287 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.284 Water bridges: A:S.50 PO4.16: 6 residues within 4Å: Chain C: T.284, V.287 Chain D: D.49, S.50, I.51, G.53 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.284 PO4.20: 5 residues within 4Å: Chain C: S.50, I.51, G.53 Chain D: T.284, V.287 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:S.50 Hydrogen bonds: D:T.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Son, H.F. et al., Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity. J.Agric.Food Chem. (2023)

Release Date

2023-12-06

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glyceraldehyde-3-phosphate dehydrogenase