SMTL ID : 8de5.1

Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Chain D: P.191 Ligands: SO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.13, A:I.13, A:Y.320 Hydrogen bonds: A:F.10, A:R.12, A:I.13, A:N.33, A:R.80, A:N.316 Water bridges: A:N.8, A:N.8, A:G.11, A:G.14, A:G.100, A:S.122, A:A.183, A:A.183 NAD.10: 25 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Chain C: P.191 Ligands: SO4.12 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.13, B:I.13, B:Y.320 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:N.33, B:R.80, B:N.316 Water bridges: B:N.8, B:N.8, B:G.11, B:G.14, B:G.100, B:S.122, B:A.183, B:A.183 NAD.19: 25 residues within 4Å: Chain B: P.191 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Ligands: SO4.21 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.13, C:I.13, C:Y.320 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.33, C:R.80, C:N.316 Water bridges: C:N.8, C:N.8, C:G.11, C:G.14, C:G.100, C:S.122, C:A.183, C:A.183 NAD.28: 25 residues within 4Å: Chain A: P.191 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, P.35, F.36, I.37, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Ligands: SO4.30 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.13, D:I.13, D:Y.320 Hydrogen bonds: D:F.10, D:R.12, D:I.13, D:N.33, D:R.80, D:N.316 Water bridges: D:N.8, D:N.8, D:G.11, D:G.14, D:G.100, D:S.122, D:A.183, D:A.183

4 x J0M: D-galactonic acid(Non-covalent)

J0M.2: 12 residues within 4Å: Chain A: S.151, C.152, T.153, T.177, H.179, S.209, S.210, T.211, A.213, A.232, R.234 Ligands: SO4.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.151, A:S.151, A:S.151, A:T.153, A:T.153, A:H.179, A:S.209, A:S.210, A:T.211, A:T.211, A:G.212, A:R.234 J0M.11: 12 residues within 4Å: Chain B: S.151, C.152, T.153, T.177, H.179, S.209, S.210, T.211, A.213, A.232, R.234 Ligands: SO4.12 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.151, B:S.151, B:S.151, B:T.153, B:T.153, B:H.179, B:S.209, B:S.210, B:T.211, B:T.211, B:G.212, B:R.234 J0M.20: 12 residues within 4Å: Chain C: S.151, C.152, T.153, T.177, H.179, S.209, S.210, T.211, A.213, A.232, R.234 Ligands: SO4.21 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.151, C:S.151, C:S.151, C:T.153, C:T.153, C:H.179, C:S.209, C:S.210, C:T.211, C:T.211, C:G.212, C:R.234 J0M.29: 12 residues within 4Å: Chain D: S.151, C.152, T.153, T.177, H.179, S.209, S.210, T.211, A.213, A.232, R.234 Ligands: SO4.30 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:S.151, D:T.153, D:T.153, D:H.179, D:S.209, D:S.210, D:T.211, D:T.211, D:G.212, D:R.234

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

SO4.3: 5 residues within 4Å: Chain A: T.182, T.184, R.234 Ligands: NAD.1, J0M.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.184, A:T.184, A:R.234 Salt bridges: A:R.234 SO4.12: 5 residues within 4Å: Chain B: T.182, T.184, R.234 Ligands: NAD.10, J0M.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.182, B:T.184 Water bridges: B:T.184, B:R.234 Salt bridges: B:R.234 SO4.21: 5 residues within 4Å: Chain C: T.182, T.184, R.234 Ligands: NAD.19, J0M.20 4 PLIP interactions: 4 interactions with chain C Water bridges: C:T.184, C:T.184, C:R.234 Salt bridges: C:R.234 SO4.30: 5 residues within 4Å: Chain D: T.182, T.184, R.234 Ligands: NAD.28, J0M.29 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.182, D:T.184 Water bridges: D:T.184, D:R.234 Salt bridges: D:R.234

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: H.24, R.322 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: D.195, R.197, S.209, S.210 Chain B: S.298 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: P.129, M.130, N.136, K.219 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: D.285, N.287, G.288, D.289, P.290 Chain C: Q.54 Ligand excluded by PLIP GOL.8: 1 residues within 4Å: Chain B: R.248 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: N.66, H.75, H.90 Ligand excluded by PLIP GOL.13: 2 residues within 4Å: Chain B: H.24, R.322 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: S.298 Chain B: D.195, R.197, S.209, S.210 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: P.129, M.130, N.136, K.219 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: D.285, N.287, G.288, D.289, P.290 Chain D: Q.54 Ligand excluded by PLIP GOL.17: 1 residues within 4Å: Chain A: R.248 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: N.66, H.75, H.90 Ligand excluded by PLIP GOL.22: 2 residues within 4Å: Chain C: H.24, R.322 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain C: D.195, R.197, S.209, S.210 Chain D: S.298 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain C: P.129, M.130, N.136, K.219 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain A: Q.54 Chain C: D.285, N.287, G.288, D.289, P.290 Ligand excluded by PLIP GOL.26: 1 residues within 4Å: Chain D: R.248 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain C: N.66, H.75, H.90 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain D: H.24, R.322 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain C: S.298 Chain D: D.195, R.197, S.209, S.210 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: P.129, M.130, N.136, K.219 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain B: Q.54 Chain D: D.285, N.287, G.288, D.289, P.290 Ligand excluded by PLIP GOL.35: 1 residues within 4Å: Chain C: R.248 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain D: N.66, H.75, H.90 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hernandez-Prieto, J.H. et al., Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie (2023)

Release Date

2023-06-21

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glyceraldehyde-3-phosphate dehydrogenase