SMTL ID : 8i4q.1

Crystal structure of 6-phosphogluconate dehydrogenase from Corynebacterium glutamicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 16 residues within 4Å: Chain A: G.14, L.15, A.16, M.18, N.37, R.38, S.39, K.42, M.78, V.79, Q.80, A.84, V.88, G.106, N.107, E.136 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:L.15, A:A.16, A:N.37, A:R.38, A:S.39, A:S.39, A:M.78, A:Q.80, A:Q.80, A:N.107, A:N.107 Water bridges: A:R.38, A:A.81, A:Q.91 Salt bridges: A:R.38, A:K.42 pi-Cation interactions: A:R.38, A:R.38 NAP.7: 17 residues within 4Å: Chain A: H.460 Chain B: G.14, L.15, A.16, M.18, N.37, R.38, S.39, K.42, M.78, V.79, Q.80, A.84, A.87, V.88, N.107, E.136 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:L.15, B:A.16, B:N.37, B:N.37, B:S.39, B:M.78, B:Q.80, B:Q.80, B:E.136 Water bridges: B:G.19, B:R.38, B:V.79, B:A.81, B:N.107, B:E.136 Salt bridges: B:R.38, B:K.42, B:K.42 pi-Cation interactions: B:R.38, B:R.38

5 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 3 residues within 4Å: Chain A: E.474, S.480, V.482 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.480, A:S.480 TRS.3: 3 residues within 4Å: Chain A: N.227, D.232, K.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.227, A:K.378 TRS.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRS.8: 7 residues within 4Å: Chain A: H.206, Y.210, L.425, P.426 Chain B: A.442, E.443, R.444 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.210, B:E.443, B:R.444 Water bridges: A:Y.210 TRS.9: 1 residues within 4Å: Chain B: E.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.385 Water bridges: B:R.382, B:R.382

7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: D.230, E.405 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.230, H2O.1, H2O.2, H2O.8 MG.10: 1 residues within 4Å: Chain B: K.350 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: R.28, N.29 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: D.230, E.405 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.230, H2O.13, H2O.14, H2O.15 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Crystal Structures of 6-Phosphogluconate Dehydrogenase from Corynebacterium glutamicum. J Microbiol Biotechnol. (2023)

Release Date

2023-07-26

Peptides

6-phosphogluconate dehydrogenase, decarboxylating: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

6-phosphogluconate dehydrogenase, decarboxylating

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