SMTL ID : 5y37.1

Crystal structure of GBS GAPDH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: N.12, G.13, F.14, G.15, R.16, I.17, N.37, D.38, L.39, E.81, R.82, A.100, T.101, G.102, F.103, F.104, T.125, A.126, C.156, N.320, Y.324 Chain D: P.195 Ligands: SO4.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.17, A:I.17, A:Y.324 Hydrogen bonds: A:F.14, A:F.14, A:R.16, A:I.17, A:N.37, A:R.82, A:T.125, A:N.320, A:N.320 Water bridges: A:N.12, A:N.12, A:G.15, A:G.18, A:G.102, A:G.187, A:G.187, A:G.187 NAD.3: 23 residues within 4Å: Chain B: N.12, G.13, F.14, G.15, R.16, I.17, N.37, D.38, L.39, E.81, R.82, A.100, T.101, G.102, F.103, F.104, T.125, A.126, C.156, N.320, Y.324 Chain C: P.195 Ligands: SO4.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.17, B:Y.324 Hydrogen bonds: B:F.14, B:R.16, B:I.17, B:R.82, B:T.125, B:N.320 Water bridges: B:N.12, B:N.12, B:G.15, B:G.18, B:G.102, B:T.125, B:G.187, B:G.187, B:G.187

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: T.186, D.188, R.203, R.239 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.186, A:D.188 Water bridges: A:G.187, A:R.203, A:R.203, A:R.203, A:R.203, A:R.239 Salt bridges: A:R.203, A:R.239 SO4.4: 5 residues within 4Å: Chain B: T.186, D.188, R.203, R.239 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.186, B:D.188 Water bridges: B:G.187, B:R.203, B:R.239, B:R.239 Salt bridges: B:R.203, B:R.239 SO4.5: 2 residues within 4Å: Chain C: R.24, S.291 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.291 Water bridges: C:R.24, C:R.24, C:S.291, C:S.291, C:R.330 Salt bridges: C:R.24 SO4.6: 4 residues within 4Å: Chain C: T.186, D.188, R.203, R.239 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.186, C:T.186, C:D.188 Salt bridges: C:R.203, C:R.239 SO4.7: 5 residues within 4Å: Chain C: S.155, T.157, T.216, G.217, A.218 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.155, C:T.157, C:T.157, C:G.217, C:A.218 Water bridges: C:S.155 SO4.8: 3 residues within 4Å: Chain A: K.302 Chain C: K.220, G.235 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Water bridges: C:T.216, C:D.234, C:D.234, A:K.302, A:K.302 Salt bridges: C:K.220, A:K.302 SO4.9: 2 residues within 4Å: Chain C: G.15, R.16 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:D.193, C:I.17, C:G.187, C:G.187 Hydrogen bonds: C:R.16 SO4.10: 4 residues within 4Å: Chain D: T.186, D.188, R.203, R.239 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.186, D:D.188 Water bridges: D:T.186, D:G.187, D:R.203, D:R.239, D:R.239 Salt bridges: D:R.203, D:R.239 SO4.11: 5 residues within 4Å: Chain D: S.155, T.157, T.216, G.217, A.218 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.155, D:T.157, D:T.216, D:G.217, D:A.218 Water bridges: D:T.157, D:T.157, D:T.157 SO4.12: 2 residues within 4Å: Chain D: G.15, R.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.16 Water bridges: D:I.17, D:G.187, D:G.187 SO4.13: 2 residues within 4Å: Chain D: D.273, R.330 7 PLIP interactions: 7 interactions with chain D Water bridges: D:D.273, D:D.273, D:R.330, D:R.330, D:R.330, D:R.330 Salt bridges: D:R.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, K. et al., High-resolution crystal structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr.,Sect.F (2018)

Release Date

2018-04-18

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