SMTL ID : 6fqz.1

Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo form, in complex with its cofactor NADP+ and in complex with its substrate 6-phosphogluconate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 6PG: 6-PHOSPHOGLUCONIC ACID(Non-covalent)

6PG.1: 16 residues within 4Å: Chain A: N.102, S.128, G.129, G.130, K.182, H.185, N.186, E.189, Y.190, A.259, K.260, R.287, I.367 Chain B: R.447, F.450, H.453 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.102, A:G.129, A:G.130, A:K.182, A:K.182, A:N.186, A:E.189, A:E.189, A:Y.190, A:K.260 Water bridges: A:R.287, A:R.287 Salt bridges: A:K.182, A:H.185, A:R.287, B:R.447, B:H.453 6PG.14: 16 residues within 4Å: Chain A: R.447, F.450, H.453 Chain B: N.102, S.128, G.129, G.130, K.182, H.185, N.186, E.189, Y.190, A.259, K.260, R.287, I.367 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.102, B:G.129, B:G.130, B:K.182, B:K.182, B:N.186, B:E.189, B:Y.190, B:Y.190, B:K.260 Water bridges: B:R.287, B:R.287 Salt bridges: B:K.182, B:H.185, B:R.287, A:R.447, A:H.453

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: M.267, A.270, T.271, I.275, P.276, C.277, C.281 Chain B: M.267, L.284, D.285, N.288 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: G.187, I.188, C.277, T.279, M.280, S.334, Q.337, G.338 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: Q.444, R.447, H.453, T.454 Chain B: K.260 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: Y.455, R.457, Y.464, T.466 Chain B: D.243, L.244, L.249 Ligands: GOL.10 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: C.281, D.285, N.288 Chain B: A.270, T.271, I.275, P.276, C.277, C.281 Ligand excluded by PLIP GOL.7: 10 residues within 4Å: Chain A: A.413, T.414, I.418, P.419, I.420, S.424 Chain B: V.410, S.424, A.428, Q.431 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: W.104, W.265 Chain B: E.272 Ligand excluded by PLIP GOL.9: 2 residues within 4Å: Chain A: L.467, W.468 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: T.466, L.467 Chain B: K.240, D.243 Ligands: GOL.5 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: I.7, Y.30, N.31, R.32, I.74, N.83 Ligand excluded by PLIP GOL.15: 11 residues within 4Å: Chain A: S.424, L.427, A.428, Q.431 Chain B: A.413, T.414, I.418, P.419, I.420, P.421, S.424 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: G.187, C.277, M.280, S.334, Q.337, G.338 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain A: N.437, L.438, P.439, N.441 Chain B: Y.200, V.201, K.204, H.205 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: D.243, L.244, L.249 Chain B: Y.455, R.457, Y.464, T.466 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: G.258, K.260 Chain B: Q.444, R.447, H.453, T.454 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: E.461, G.462, N.463 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain A: E.300 Chain B: S.435, Q.436, N.437 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: Y.171, I.172, G.173, W.351, K.352 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: S.22, E.47, L.49, R.135, Y.136 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 5 residues within 4Å: Chain A: K.260, G.261, K.264 Chain B: E.272, G.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.264 PEG.13: 12 residues within 4Å: Chain A: P.278, C.281, A.282, D.285, P.421, S.424, A.425 Chain B: P.278, C.281, A.282, D.285, A.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.285, A:S.424, A:A.425 PEG.25: 4 residues within 4Å: Chain B: G.462, N.463, Y.464, H.465 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.465, B:H.465 PEG.26: 3 residues within 4Å: Chain B: V.163, V.371, D.374 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.24: 7 residues within 4Å: Chain A: E.272, G.274 Chain B: A.259, K.260, G.261, K.264, W.265 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.264, A:E.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haeussler, K. et al., Characterization of Plasmodium falciparum 6-Phosphogluconate Dehydrogenase as an Antimalarial Drug Target. J. Mol. Biol. (2018)

Release Date

2018-08-22

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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