SMTL ID : 6fzh.1

Crystal structure of a streptococcal dehydrogenase at 1.5 Angstroem resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, R.78, A.96, T.97, G.98, F.99, F.100, T.121, A.122, C.152, T.182, N.316, Y.320 Chain C: P.191 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.13, A:I.13, A:Y.320 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:R.78, A:T.121, A:N.316 Water bridges: A:N.8, A:N.8, A:G.11, A:G.14, A:R.78, A:G.98, A:G.183, A:G.183 NAD.3: 23 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, R.78, A.96, T.97, G.98, F.99, F.100, T.121, A.122, C.152, T.182, N.316, Y.320 Chain D: P.191 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.13, B:I.13, B:Y.320 Hydrogen bonds: B:F.10, B:F.10, B:R.12, B:I.13, B:R.78, B:N.316 Water bridges: B:N.8, B:N.8, B:G.11, B:G.14, B:R.78, B:G.98, B:T.121, B:G.183, B:G.183 NAD.7: 23 residues within 4Å: Chain A: P.191 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, R.78, A.96, T.97, G.98, F.99, F.100, T.121, A.122, C.152, T.182, N.316, Y.320 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.13, C:I.13, C:Y.320 Hydrogen bonds: C:F.10, C:F.10, C:R.12, C:I.13, C:R.78, C:T.121, C:N.316 Water bridges: C:N.8, C:N.8, C:G.11, C:G.14, C:R.78, C:G.98, C:T.121, C:G.183, C:G.183 NAD.9: 23 residues within 4Å: Chain B: P.191 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, R.78, A.96, T.97, G.98, F.99, F.100, T.121, A.122, C.152, T.182, N.316, Y.320 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.13, D:I.13, D:Y.320 Hydrogen bonds: D:F.10, D:F.10, D:R.12, D:I.13, D:R.78, D:N.316 Water bridges: D:N.8, D:N.8, D:G.11, D:G.14, D:R.78, D:G.98, D:T.121, D:G.183, D:G.183

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.39, H.43, K.46, Y.47 Chain D: D.276 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:D.276, A:N.39, A:N.39, A:K.46 Water bridges: A:K.46 GOL.5: 7 residues within 4Å: Chain B: P.123, S.151, T.154, T.212, G.213, A.214, A.217 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.151, B:S.151, B:T.212, B:G.213 Water bridges: B:S.151, B:A.214 GOL.6: 7 residues within 4Å: Chain A: T.295, Q.296 Chain B: R.198, P.209, N.210, S.211, A.232 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.198, B:R.198, A:T.295 Water bridges: B:A.233, A:Q.296, A:Q.296 GOL.8: 5 residues within 4Å: Chain B: D.276 Chain C: N.39, H.43, K.46, Y.47 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.276, C:N.39, C:N.39, C:K.46 Water bridges: C:K.46 GOL.11: 7 residues within 4Å: Chain D: P.123, S.151, T.154, T.212, G.213, A.214, A.217 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:T.212, D:G.213 Water bridges: D:S.151, D:A.214 GOL.12: 7 residues within 4Å: Chain C: T.295, Q.296 Chain D: R.198, P.209, N.210, S.211, A.232 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.198, D:R.198, C:T.295 Water bridges: D:A.233, C:Q.296, C:Q.296

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

PEG.4: 3 residues within 4Å: Chain B: N.134, H.137, N.268 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.268 Water bridges: B:N.134, B:T.135, B:D.138, B:A.266, B:A.266, B:N.268 PEG.10: 3 residues within 4Å: Chain D: N.134, H.137, N.268 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.268 Water bridges: D:N.134, D:T.135, D:D.138, D:A.266, D:A.266, D:N.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomez, S. et al., The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding. Front Microbiol (2019)

Release Date

2019-03-27

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