SMTL ID : 6utm.1

Native E. coli Glyceraldehyde 3-phosphate dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

4 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.1: 10 residues within 4Å: Chain A: V.130, K.131, G.132, A.133, N.134, F.135, D.136, K.159, E.266, M.267 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.132, A:A.133, A:F.135, A:D.136, A:E.266 G3P.4: 7 residues within 4Å: Chain B: V.130, K.131, G.132, A.133, N.134, F.135, D.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.132, B:G.132, B:A.133, B:F.135, B:D.136, B:D.136 G3P.8: 10 residues within 4Å: Chain C: V.130, K.131, G.132, A.133, N.134, F.135, D.136, K.159, E.266, M.267 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.132, C:A.133, C:F.135, C:D.136, C:E.266 G3P.11: 7 residues within 4Å: Chain D: V.130, K.131, G.132, A.133, N.134, F.135, D.136 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.132, D:G.132, D:A.133, D:F.135, D:D.136, D:D.136

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: A.20, R.23, I.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.23 Water bridges: A:R.23 NA.3: 4 residues within 4Å: Chain A: E.76, R.77, D.78, N.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.76, A:R.77, A:D.78, A:N.81 NA.7: 3 residues within 4Å: Chain B: A.20, R.23, I.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.20, B:R.23 Water bridges: B:I.28 NA.9: 3 residues within 4Å: Chain C: A.20, R.23, I.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.23 Water bridges: C:R.23 NA.10: 4 residues within 4Å: Chain C: E.76, R.77, D.78, N.81 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.76, C:R.77, C:D.78, C:D.78, C:N.81 NA.14: 3 residues within 4Å: Chain D: A.20, R.23, I.26 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.23, D:I.26 Water bridges: D:I.28

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: T.126, P.127, M.128, N.134, K.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.128, B:N.134 Water bridges: B:S.122 GOL.6: 5 residues within 4Å: Chain B: N.162, D.163, F.165, G.166, E.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.162, B:F.165 Water bridges: B:N.162 GOL.12: 5 residues within 4Å: Chain D: T.126, P.127, M.128, N.134, K.216 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.128, D:N.134 Water bridges: D:S.122 GOL.13: 5 residues within 4Å: Chain D: N.162, D.163, F.165, G.166, E.247 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.162, D:F.165, D:E.247 Water bridges: D:N.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodriguez-Hernandez, A. et al., A Novel Substrate-Binding Site in the X-Ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion. Crystals (2019)

Release Date

2019-12-11

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

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