SMTL ID : 5ld5.1

Crystal structure of a bacterial dehydrogenase at 2.19 Angstroms resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 20 residues within 4Å: Chain A: G.26, F.27, G.28, R.29, I.30, N.50, D.51, L.52, E.96, A.97, C.115, T.116, G.117, F.118, S.139, A.140, C.170, N.338, Y.342 Chain B: P.209 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.30, A:Y.342 Hydrogen bonds: A:F.27, A:F.27, A:R.29, A:I.30, A:A.97, A:N.338 Water bridges: A:N.25, A:N.25, A:G.28, A:G.117, A:S.139, A:G.201, A:G.201, A:D.202 NAD.6: 20 residues within 4Å: Chain A: P.209 Chain B: G.26, F.27, G.28, R.29, I.30, N.50, D.51, L.52, E.96, A.97, C.115, T.116, G.117, F.118, S.139, A.140, C.170, N.338, Y.342 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.30, B:Y.342 Hydrogen bonds: B:F.27, B:F.27, B:R.29, B:I.30, B:A.97 Water bridges: B:G.28, B:N.50, B:G.117, B:S.139, B:G.201 NAD.12: 21 residues within 4Å: Chain C: G.26, F.27, G.28, R.29, I.30, N.50, D.51, L.52, E.96, A.97, C.115, T.116, G.117, F.118, S.139, A.140, C.170, T.200, N.338, Y.342 Chain D: P.209 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.30, C:Y.342 Hydrogen bonds: C:F.27, C:R.29, C:I.30, C:A.97 Water bridges: C:N.25, C:G.28, C:G.31, C:G.117, C:G.117, C:Y.119 NAD.15: 20 residues within 4Å: Chain C: P.209 Chain D: G.26, F.27, G.28, R.29, I.30, N.50, D.51, L.52, E.96, A.97, C.115, T.116, G.117, F.118, S.139, A.140, C.170, N.338, Y.342 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.30, D:Y.342 Hydrogen bonds: D:F.27, D:F.27, D:R.29, D:I.30, D:A.97 Water bridges: D:N.25, D:G.28, D:R.32, D:G.117, D:Y.119, D:S.139, D:G.201, D:G.201, D:G.201, D:G.201, D:N.338

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Y.64, N.70, R.73 Chain D: D.303, I.304, M.307, Y.309, L.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.70, A:R.73 GOL.3: 4 residues within 4Å: Chain A: R.36, N.70, Y.71, N.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.71, A:N.74 GOL.4: 5 residues within 4Å: Chain A: P.141, S.169, T.230, G.231, A.232 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.169, A:T.230, A:G.231, A:G.231, A:A.232 GOL.5: 5 residues within 4Å: Chain A: A.222, P.255 Chain B: P.255 Chain C: A.222 Chain D: A.222 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:A.222, B:P.255, A:P.255 GOL.7: 8 residues within 4Å: Chain B: D.303, I.304, M.307, Y.309, L.312 Chain C: Y.64, N.70, R.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.70 GOL.8: 6 residues within 4Å: Chain B: T.316 Chain D: R.216, P.227, N.228, S.229, S.250 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.316, B:T.316, D:R.216 GOL.9: 5 residues within 4Å: Chain B: N.152, V.153, N.154, H.155, E.156 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.152, B:H.155, B:E.156, B:E.156 GOL.10: 9 residues within 4Å: Chain B: Y.64, N.70, R.73 Chain C: I.299, D.303, I.304, M.307, Y.309, L.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.64, B:N.70, B:R.73 GOL.11: 5 residues within 4Å: Chain B: R.216, P.227, N.228 Chain D: T.316, Q.317 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.216, B:P.227, B:N.228, D:T.316 GOL.13: 6 residues within 4Å: Chain A: T.316 Chain C: R.216, P.227, N.228, S.229, S.250 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.216, C:P.227 Water bridges: C:S.250, C:S.250 GOL.14: 6 residues within 4Å: Chain C: V.276, N.280, A.315, T.316, Q.317, T.318 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.280 GOL.16: 5 residues within 4Å: Chain A: D.303, M.307, Y.309 Chain D: N.70, R.73 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.70, D:R.73, D:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Querol-Garcia, J. et al., Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin. Front Microbiol (2017)

Release Date

2017-07-12

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