SMTL ID : 7zhx.1

Leishmania donovani Glucose 6-Phosphate Dehydrogenase (N-terminal deletion variant)complexed with NADP(H)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: C.92, G.93, A.94, D.100, R.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.94, A:R.103, A:R.103 Water bridges: A:C.92 PEG.8: 5 residues within 4Å: Chain A: R.361, D.362, E.363, V.364 Chain B: R.209 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.361, A:V.364, B:R.209 Water bridges: A:E.363, A:H.365, A:R.373 PEG.11: 5 residues within 4Å: Chain B: C.92, G.93, A.94, D.100, R.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.94, B:R.103, B:R.103 Water bridges: B:C.92 PEG.18: 5 residues within 4Å: Chain A: R.209 Chain B: R.361, D.362, E.363, V.364 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.361, B:V.364, A:R.209 Water bridges: B:E.363, B:H.365, B:R.373

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 10 residues within 4Å: Chain A: V.4, E.7, Q.8, R.11, N.123, W.154, R.156, L.433, L.434, G.435 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.11, A:R.156, A:R.156 Water bridges: A:N.123, A:N.123, A:N.123 PG4.12: 10 residues within 4Å: Chain B: V.4, E.7, Q.8, R.11, N.123, W.154, R.156, L.433, L.434, G.435 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.11, B:R.156, B:R.156 Water bridges: B:N.123, B:N.123, B:N.123

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: K.195, V.198, Q.199, D.431, N.436, N.439 Chain B: L.401 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.199 Water bridges: A:N.436, A:N.439 EDO.4: 3 residues within 4Å: Chain A: N.216, D.334, R.335 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.218, A:R.335 EDO.5: 9 residues within 4Å: Chain A: I.285, E.286, P.287, I.288, T.289, N.292, R.328, L.329, N.330 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.289, A:T.289, A:N.292, A:N.330, A:N.330 EDO.6: 6 residues within 4Å: Chain A: R.205, F.206, S.212, W.215, K.265, R.335 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.205, A:S.212, A:K.265, A:R.335 Water bridges: A:E.264, A:R.335 EDO.7: 8 residues within 4Å: Chain A: R.165, D.241, N.242, I.243, G.244, R.247, P.322, D.461 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.165, A:I.243, A:R.247, A:R.247, A:D.461 EDO.9: 5 residues within 4Å: Chain A: C.284, I.285, E.286, N.330, N.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.286, A:N.330, A:N.332 EDO.13: 7 residues within 4Å: Chain A: L.401 Chain B: K.195, V.198, Q.199, D.431, N.436, N.439 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.199 Water bridges: B:N.436, B:N.439 EDO.14: 3 residues within 4Å: Chain B: N.216, D.334, R.335 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.218, B:R.335 EDO.15: 9 residues within 4Å: Chain B: I.285, E.286, P.287, I.288, T.289, N.292, R.328, L.329, N.330 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.289, B:T.289, B:N.292, B:N.330, B:N.330 EDO.16: 6 residues within 4Å: Chain B: R.205, F.206, S.212, W.215, K.265, R.335 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.205, B:S.212, B:K.265, B:R.335 Water bridges: B:E.264, B:R.335 EDO.17: 8 residues within 4Å: Chain B: R.165, D.241, N.242, I.243, G.244, R.247, P.322, D.461 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.165, B:I.243, B:R.247, B:R.247, B:D.461 EDO.19: 5 residues within 4Å: Chain B: C.284, I.285, E.286, N.330, N.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.286, B:N.330, B:N.332

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

NDP.10: 18 residues within 4Å: Chain A: G.19, S.21, G.22, D.23, L.24, K.28, A.52, R.53, T.54, Y.95, A.129, L.130, P.131, P.132, V.134, E.160, K.161, P.162 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.21, A:S.21, A:D.23, A:L.24, A:K.28, A:R.53, A:T.54, A:T.54, A:T.54, A:Y.95, A:Y.95, A:L.130 Water bridges: A:D.23, A:A.25, A:R.53, A:R.53, A:S.133 Salt bridges: A:R.53, A:E.160 pi-Cation interactions: A:R.53 NDP.20: 18 residues within 4Å: Chain B: G.19, S.21, G.22, D.23, L.24, K.28, A.52, R.53, T.54, Y.95, A.129, L.130, P.131, P.132, V.134, E.160, K.161, P.162 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.21, B:S.21, B:D.23, B:L.24, B:K.28, B:R.53, B:T.54, B:T.54, B:T.54, B:Y.95, B:Y.95, B:L.130 Water bridges: B:D.23, B:A.25, B:R.53, B:R.53, B:S.133 Salt bridges: B:R.53, B:E.160 pi-Cation interactions: B:R.53

Links

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Citation

Berneburg, I. et al., Crystal structure of Leishmania donovani glucose 6-phosphate dehydrogenase reveals a unique N-terminal domain. Commun Biol (2022)

Release Date

2022-12-14

Peptides

Glucose-6-phosphate 1-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glucose-6-phosphate 1-dehydrogenase