SMTL ID : 1pgn.1

CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Y.191, G.258, Q.259, K.260, T.262, R.287 Chain B: R.446 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.258, A:K.260 Water bridges: A:R.287, A:R.287 Salt bridges: A:R.287, B:R.446, B:H.452 SO4.2: 3 residues within 4Å: Chain A: G.211, H.212, H.248 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.212 Water bridges: A:H.212, A:K.213, A:H.248, A:H.248, A:H.248 Salt bridges: A:H.212, A:K.213, A:H.248 SO4.5: 7 residues within 4Å: Chain A: R.446 Chain B: Y.191, G.258, Q.259, K.260, T.262, R.287 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Salt bridges: A:R.446, A:H.452, B:R.287 Hydrogen bonds: B:Y.191, B:G.258, B:K.260 Water bridges: B:R.287, B:R.287 SO4.6: 3 residues within 4Å: Chain B: G.211, H.212, H.248 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.212 Water bridges: B:K.213, B:K.213, B:H.248 Salt bridges: B:H.212, B:K.213, B:H.248

2 x NBP: NICOTINAMIDE 8-BROMO-ADENINE DINUCLEOTIDE PHOSPHATE(Non-covalent)

NBP.3: 17 residues within 4Å: Chain A: G.9, L.10, A.11, V.12, M.13, N.32, R.33, T.34, V.74, K.75, A.79, F.83, G.100, G.101, N.102, E.131 Ligands: POP.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.10, A:M.13, A:N.32, A:R.33, A:R.33, A:R.33, A:T.34, A:T.34, A:K.75, A:K.75, A:N.102, A:N.102, A:E.131 Salt bridges: A:R.33, A:K.75 pi-Cation interactions: A:R.33, A:R.33 NBP.7: 17 residues within 4Å: Chain B: G.9, L.10, A.11, V.12, M.13, N.32, R.33, T.34, V.74, K.75, A.79, F.83, G.100, G.101, N.102, E.131 Ligands: POP.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.10, B:M.13, B:N.32, B:R.33, B:R.33, B:T.34, B:K.75, B:K.75, B:N.102, B:N.102, B:E.131, B:E.131 Salt bridges: B:R.33, B:K.75 pi-Cation interactions: B:R.33, B:R.33

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 10 residues within 4Å: Chain A: M.13, N.102, V.127, S.128, G.129, G.130, K.183, N.187, I.366 Ligands: NBP.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.102, A:V.127, A:G.129, A:G.129, A:G.130, A:N.187, A:N.187 Salt bridges: A:K.183, A:K.183 POP.8: 10 residues within 4Å: Chain B: M.13, N.102, V.127, S.128, G.129, G.130, K.183, N.187, I.366 Ligands: NBP.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.102, B:V.127, B:G.129, B:G.129, B:G.130, B:N.187, B:N.187 Salt bridges: B:K.183, B:K.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, M.J. et al., Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. Structure (1994)

Release Date

1995-02-27

Peptides

6-PHOSPHOGLUCONATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

6-PHOSPHOGLUCONATE DEHYDROGENASE

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