SMTL ID : 6fzi.1

Crystal Structure of a Clostridial Dehydrogenase at 2.55 Angstroems Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: N.7, G.8, G.10, R.11, I.12, N.32, D.33, L.34, K.76, S.77, C.95, T.96, G.97, F.98, F.99, S.119, A.120, C.150, N.181, N.314, Y.318 Chain B: P.189 Ligands: PEG.6, ACT.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.318 Hydrogen bonds: A:R.11, A:I.12, A:N.32, A:S.77, A:N.181, A:N.314 NAD.8: 24 residues within 4Å: Chain A: P.189 Chain B: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, K.76, S.77, C.95, T.96, G.97, F.98, F.99, S.119, A.120, C.150, N.181, N.314, Y.318 Ligands: PEG.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.318 Hydrogen bonds: B:F.9, B:F.9, B:R.11, B:I.12, B:N.32, B:S.77, B:N.181, B:N.314 NAD.17: 21 residues within 4Å: Chain C: G.8, G.10, R.11, I.12, N.32, D.33, L.34, K.76, S.77, C.95, T.96, G.97, F.98, F.99, S.119, A.120, C.150, N.181, N.314, Y.318 Chain D: P.189 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.318 Hydrogen bonds: C:R.11, C:I.12, C:N.32, C:S.77, C:N.181, C:N.314 Water bridges: C:E.315 NAD.22: 22 residues within 4Å: Chain C: P.189 Chain D: N.7, G.8, G.10, R.11, I.12, N.32, D.33, L.34, K.76, S.77, C.95, T.96, G.97, F.98, F.99, S.119, A.120, C.150, N.181, N.314, Y.318 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.318 Hydrogen bonds: D:R.11, D:I.12, D:N.32, D:S.77, D:N.181, D:N.314 Water bridges: D:D.182

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.196, N.208, S.209 Chain C: T.293, K.296 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.196, A:N.208, A:N.230, C:K.296, C:K.296 GOL.3: 6 residues within 4Å: Chain A: A.202 Chain B: A.202, P.235 Chain C: A.202 Chain D: A.202, P.235 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:A.202, A:A.202 Water bridges: D:A.202 GOL.4: 6 residues within 4Å: Chain A: L.248, D.249, K.251, G.302, Q.303, Q.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.249, A:Q.304, A:Q.304 GOL.5: 4 residues within 4Å: Chain A: H.42, K.45, I.57 Chain D: D.274 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.45, A:I.57, D:D.274 GOL.9: 8 residues within 4Å: Chain B: R.196, N.208, S.209, N.230 Chain D: T.293, Q.294, K.296 Ligands: GOL.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.196, B:S.209, B:N.230, D:K.296 GOL.10: 6 residues within 4Å: Chain B: G.193, D.194, L.195, R.196 Chain D: P.275 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.195 GOL.18: 1 residues within 4Å: Chain C: N.165 No protein-ligand interaction detected (PLIP) GOL.19: 5 residues within 4Å: Chain C: E.267, N.320, I.323, R.324, K.327 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.267, C:R.324, C:R.324, C:K.327 GOL.20: 2 residues within 4Å: Chain C: D.164, N.165 No protein-ligand interaction detected (PLIP) GOL.21: 6 residues within 4Å: Chain A: T.293 Chain C: R.196, P.207, N.208, S.209, N.230 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.196, C:P.207, C:S.209, C:N.230 GOL.23: 6 residues within 4Å: Chain B: T.293, K.296 Chain D: R.196, N.208, S.209 Ligands: ACT.25 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.196, B:K.296

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

PEG.6: 5 residues within 4Å: Chain A: T.180, N.181, D.182, R.233 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.181, A:D.182 Water bridges: A:N.181 PEG.11: 4 residues within 4Å: Chain B: C.150, T.180, D.182 Ligands: NAD.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.182

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain A: F.98 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) ACT.12: 5 residues within 4Å: Chain B: L.248, K.251, G.302, Q.303, Q.304 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.304 ACT.13: 3 residues within 4Å: Chain B: H.42, K.45 Chain C: D.274 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.45 ACT.14: 4 residues within 4Å: Chain B: V.133, N.134, H.135, D.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.135, B:D.136, B:D.136 Salt bridges: B:H.135 ACT.15: 3 residues within 4Å: Chain B: I.284, S.285 Chain C: R.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.285 ACT.16: 1 residues within 4Å: Chain B: F.286 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.286 ACT.24: 5 residues within 4Å: Chain D: N.132, V.133, N.134, H.135, D.136 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.133, D:H.135, D:D.136 Salt bridges: D:H.135 ACT.25: 5 residues within 4Å: Chain B: P.275 Chain D: G.193, D.194, L.195 Ligands: GOL.23 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.38 Hydrogen bonds: D:L.195 ACT.26: 5 residues within 4Å: Chain D: N.23, E.267, N.320, R.324, K.327 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.320 Salt bridges: D:R.324, D:K.327

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
C

D
D

Glyceraldehyde-3-phosphate dehydrogenase