SMTL ID : 8hrt.1

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K/F100V/P192S) in complex with NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 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, V.100, F.101, S.121, A.122, C.153, N.315, Y.319 Chain C: S.192 26 PLIP interactions: 21 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.13, A:Y.319 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:N.34, A:S.36, A:K.37, A:R.79, A:N.315, C:S.192, C:S.192 Water bridges: A:N.8, A:N.8, A:G.11, A:G.14, A:G.99, A:S.121, A:G.184, A:G.184, A:E.316, C:R.187, C:S.192, C:S.192 Salt bridges: A:K.37 NAP.4: 23 residues within 4Å: Chain B: 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, V.100, F.101, S.121, A.122, C.153, T.183, N.315, Y.319 Chain D: S.192 32 PLIP interactions: 24 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:I.13, B:Y.319 Hydrogen bonds: B:F.10, B:F.10, B:R.12, B:I.13, B:N.34, B:D.35, B:S.36, B:S.36, B:R.79, B:N.315, B:N.315, D:S.192, D:S.192 Water bridges: B:N.8, B:N.8, B:G.11, B:G.14, B:G.99, B:G.184, B:G.184, B:G.184, B:G.184, B:E.316, D:R.187, D:R.187, D:R.187, D:R.187, D:S.192, D:S.192 Salt bridges: B:K.37 NAP.7: 22 residues within 4Å: Chain A: S.192 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.101, S.121, A.122, C.153, T.183, N.315, Y.319 28 PLIP interactions: 25 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.13, C:I.13, C:Y.319 Hydrogen bonds: C:F.10, C:F.10, C:R.12, C:I.13, C:N.34, C:D.35, C:S.36, C:S.36, C:R.79, C:N.315, C:N.315, A:S.192 Water bridges: C:N.8, C:N.8, C:G.11, C:G.14, C:G.99, C:S.121, C:G.184, C:G.184, C:G.184, C:G.184, A:R.187, A:S.192 Salt bridges: C:K.37 NAP.9: 23 residues within 4Å: Chain B: S.192 Chain D: 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, V.100, F.101, S.121, A.122, C.153, T.183, N.315, Y.319 27 PLIP interactions: 21 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:I.13, D:I.13, D:Y.319 Hydrogen bonds: D:F.10, D:R.12, D:I.13, D:N.34, D:S.36, D:S.36, D:R.79, D:N.315, B:S.192, B:S.192 Water bridges: D:N.8, D:G.11, D:G.14, D:G.99, D:S.121, D:G.184, D:G.184, D:G.184, D:G.184, B:R.187, B:R.187, B:S.192, B:S.192 Salt bridges: D:K.37

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.24, S.25, D.26, D.27, E.328 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.25, A:D.26 Water bridges: A:E.328 GOL.3: 6 residues within 4Å: Chain A: D.38, N.39, K.40, Y.61, D.62, D.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.38, A:N.39, A:K.40, A:D.63 Water bridges: A:D.63 GOL.6: 7 residues within 4Å: Chain A: R.54 Chain B: A.275, Y.276, S.277, E.279, D.289, H.291 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.276, B:S.277, B:S.277, B:D.289, A:R.54, A:R.54 GOL.8: 5 residues within 4Å: Chain C: L.22, E.23, L.55, G.56, Q.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.56, C:G.56, C:Q.57

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

EDO.5: 6 residues within 4Å: Chain B: V.302, S.303 Chain C: K.215, G.226, L.228, D.229 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:L.228, B:V.302 Water bridges: C:K.215, B:V.302, B:V.302

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
C

D
D

Glyceraldehyde-3-phosphate dehydrogenase