SMTL ID : 7xzg.1

High resolution crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans complexed with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.78, R.79, S.97, T.98, G.99, F.101, T.121, A.122, C.151, A.182, N.315, E.316, Y.319 Chain C: P.190 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.319 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:N.33, A:R.79, A:N.315 Water bridges: A:N.8, A:N.8, A:G.11, A:G.14, A:R.15, A:G.99, A:T.121, A:A.182, A:A.182 NAD.5: 25 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.78, R.79, S.97, T.98, G.99, F.101, T.121, A.122, C.151, A.182, N.315, E.316, Y.319 Chain D: P.190 21 PLIP interactions: 21 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:N.33, B:R.79, B:N.315 Water bridges: B:N.8, B:N.8, B:F.10, B:G.11, B:G.14, B:R.15, B:G.99, B:T.121, B:A.182, B:A.182, B:E.316, B:E.316 NAD.8: 25 residues within 4Å: Chain A: P.190 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.78, R.79, S.97, T.98, G.99, F.101, T.121, A.122, C.151, A.182, N.315, E.316, Y.319 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.13, C:Y.319 Hydrogen bonds: C:F.10, C:F.10, C:R.12, C:I.13, C:N.33, C:R.79, C:T.121, C:N.315, C:N.315 Water bridges: C:N.8, C:N.8, C:G.11, C:G.14, C:R.15, C:G.99, C:T.121, C:A.182, C:A.182 NAD.10: 25 residues within 4Å: Chain B: P.190 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.78, R.79, S.97, T.98, G.99, F.101, T.121, A.122, C.151, A.182, N.315, E.316, Y.319 20 PLIP interactions: 20 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:N.33, D:R.79, D:T.121, D:N.315, D:N.315 Water bridges: D:N.8, D:N.8, D:G.11, D:G.14, D:G.99, D:T.121, D:A.182, D:A.182 pi-Stacking: D:F.36

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

EDO.2: 4 residues within 4Å: Chain A: P.128, M.129, N.135, K.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.129, A:N.135 EDO.3: 5 residues within 4Å: Chain A: K.270, G.271, V.272, R.322, D.325 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.322 EDO.4: 6 residues within 4Å: Chain A: R.54 Chain B: Y.275, T.276, F.285, Y.290, I.293 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:Y.275, B:T.276, B:Y.290 Hydrogen bonds: A:R.54, A:R.54 EDO.6: 4 residues within 4Å: Chain B: K.270, V.272, R.322, D.325 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.322 EDO.7: 5 residues within 4Å: Chain B: V.100, F.101, T.102, K.103, G.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.102, B:T.102, B:K.103, B:G.106 EDO.9: 6 residues within 4Å: Chain A: R.196, P.207, S.208, M.230 Chain D: K.297, A.298 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:A.298, A:R.196, A:R.196 Water bridges: A:S.208 EDO.11: 4 residues within 4Å: Chain D: P.128, M.129, N.135, K.218 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.129, D:N.135 EDO.12: 4 residues within 4Å: Chain D: A.258, Q.259, Y.275, E.277 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain D: D.194, G.197, I.206, P.207, S.208, R.233 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.207, D:S.208 Water bridges: D:S.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., High resolution crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans complexed with NAD+. To Be Published

Release Date

2023-06-07

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

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