SMTL ID : 1pgo.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 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: Y.191, Q.259, K.260, G.261, T.262, R.287 Chain B: R.446, H.452 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.258, A:K.260, A:G.261, A:T.262 Water bridges: A:E.190, A:R.287 Salt bridges: A:R.287, B:R.446, B:H.452 SO4.2: 4 residues within 4Å: Chain A: G.211, H.212, K.213, H.248 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.212, A:K.213 Water bridges: A:H.248, A:H.248 Salt bridges: A:H.212, A:H.248 SO4.4: 8 residues within 4Å: Chain A: R.446, H.452 Chain B: Y.191, Q.259, K.260, G.261, T.262, R.287 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.191, B:G.258, B:K.260, B:G.261 Water bridges: B:R.287, B:R.287 Salt bridges: B:R.287, A:R.446, A:H.452 SO4.5: 4 residues within 4Å: Chain B: G.211, H.212, K.213, H.248 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.212, B:K.213 Water bridges: B:H.248 Salt bridges: B:H.212, B:H.248

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.3: 21 residues within 4Å: Chain A: G.9, L.10, A.11, M.13, N.32, R.33, T.34, V.74, K.75, A.79, F.83, N.102, V.127, S.128, G.129, G.130, K.183, H.186, N.187, E.190, I.366 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.366 Hydrogen bonds: A:L.10, A:A.11, A:N.32, A:R.33, A:R.33, A:T.34, A:T.34, A:K.75, A:N.102, A:K.183, A:N.187, A:E.190 Water bridges: A:M.13, A:M.13, A:G.14, A:N.102 Salt bridges: A:R.33, A:K.75 pi-Cation interactions: A:R.33, A:R.33, A:K.183 NDP.6: 21 residues within 4Å: Chain B: G.9, L.10, A.11, M.13, N.32, R.33, T.34, V.74, K.75, A.79, F.83, N.102, V.127, S.128, G.129, G.130, K.183, H.186, N.187, E.190, I.366 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.366 Hydrogen bonds: B:L.10, B:A.11, B:N.32, B:R.33, B:R.33, B:T.34, B:K.75, B:N.102, B:K.183, B:N.187, B:E.190 Water bridges: B:M.13, B:M.13, B:G.14, B:N.102 Salt bridges: B:R.33, B:K.75 pi-Cation interactions: B:R.33, B:R.33, 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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