SMTL ID : 7zhy.1

Leishmania donovani Glucose 6-Phosphate Dehydrogenase C138S mutant complexed with NADP(H)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 17 residues within 4Å: Chain A: G.78, S.80, G.81, D.82, L.83, A.111, R.112, T.113, Y.154, A.188, L.189, P.190, P.191, V.193, E.219, K.220, P.221 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.80, A:D.82, A:L.83, A:R.112, A:T.113, A:T.113, A:T.113, A:Y.154, A:L.189 Water bridges: A:D.82, A:D.82, A:A.84, A:R.112, A:R.112, A:S.192 Salt bridges: A:R.112 pi-Cation interactions: A:R.112 NDP.22: 18 residues within 4Å: Chain B: G.78, S.80, G.81, D.82, L.83, A.111, R.112, T.113, Y.154, A.188, L.189, P.190, P.191, V.193, E.219, K.220, P.221 Ligands: EDO.26 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.80, B:D.82, B:D.82, B:L.83, B:R.112, B:T.113, B:T.113, B:T.113, B:Y.154, B:Y.154, B:L.189 Water bridges: B:A.84, B:R.112, B:R.112 Salt bridges: B:R.112, B:E.219 pi-Cation interactions: B:R.112

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

EDO.2: 2 residues within 4Å: Chain A: E.541, N.545 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: R.224, D.300, N.301, I.302, R.306, P.381, D.520 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: N.275, D.393, R.394 Ligands: EDO.13, EDO.15 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: D.155, V.157, S.196, E.199, S.200 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: R.112 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: Q.310, N.311, T.314, Q.315, L.341, V.500, E.504, A.508 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: R.168, Q.208, E.209, V.210 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: N.275, A.276, S.277, D.393, R.394 Ligands: EDO.6 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: R.394 Ligands: EDO.6 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: C.352, V.353, L.354, I.524, K.525, I.527 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: R.268 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: E.443, T.471, H.473 Chain B: K.452, P.454 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: E.541, N.545 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: K.220, P.221, I.302, R.306, D.307, N.311 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: R.112, T.113 Ligands: NDP.22 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: L.460 Chain B: K.254, V.257, Q.258, D.490, N.495, N.498 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: K.86, K.128, Y.129 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain B: R.224, D.300, N.301, I.302, G.303, R.306, P.381, D.520 Ligands: EDO.36 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: N.275, D.393, R.394 Ligands: EDO.40 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: R.416, Y.446, K.448, E.467 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: R.264, F.265, S.271, W.274, R.394 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: T.379, C.380, I.519, D.520 Ligands: EDO.31 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: R.168, Q.208, E.209, V.210 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: Q.27, R.31, N.132, L.133, S.134 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain B: Q.310, N.311, T.314, Q.315, L.341, V.500, E.504, A.508 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: N.275, A.276, S.277, D.393, R.394 Ligands: EDO.33 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: D.155, V.157, E.199, K.203 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain B: K.114, V.115, D.116, D.117 Ligand excluded by PLIP

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

SO4.3: 4 residues within 4Å: Chain A: R.420, D.421, R.432, K.549 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.421 Water bridges: A:R.420, A:R.420 Salt bridges: A:R.420, A:R.432, A:K.549 SO4.18: 5 residues within 4Å: Chain A: T.285, K.287, K.403, R.416, R.534 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Q.283, A:T.285, A:R.416 Salt bridges: A:K.287, A:K.403, A:R.416, A:R.534 SO4.19: 8 residues within 4Å: Chain A: R.31, K.32, P.33, D.34, H.464, Q.465, T.466, E.467 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Water bridges: B:H.473, A:K.32, A:D.35 Hydrogen bonds: A:D.34, A:E.467 Salt bridges: A:R.31, A:H.464 SO4.20: 4 residues within 4Å: Chain A: R.416, E.434, Y.446, K.448 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.446 Salt bridges: A:R.416, A:K.448 SO4.24: 4 residues within 4Å: Chain B: R.420, D.421, R.432, K.549 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.421 Water bridges: B:R.432 Salt bridges: B:R.432, B:K.549 SO4.27: 6 residues within 4Å: Chain B: Q.283, T.285, K.287, K.403, R.534 Ligands: PEG.29 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.283 Water bridges: B:Q.283, B:Q.283 Salt bridges: B:K.287, B:K.403, B:R.534 SO4.43: 4 residues within 4Å: Chain B: T.348, K.349, E.350, Q.518 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.349, B:E.350, B:Q.518 Water bridges: B:K.349, B:K.349 Salt bridges: B:K.349

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

PEG.5: 10 residues within 4Å: Chain A: K.254, Q.258, L.328, A.330, I.333, D.490, N.495, T.497, N.498 Chain B: L.460 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.328, A:D.490, A:N.495, A:T.497, A:N.498, B:L.460 Water bridges: A:N.498 PEG.7: 1 residues within 4Å: Chain A: K.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.114 Water bridges: A:K.114 PEG.11: 6 residues within 4Å: Chain A: F.150, C.151, G.152, A.153, D.159, R.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.151, A:R.162, A:R.162 PEG.29: 3 residues within 4Å: Chain B: R.534, H.550 Ligands: SO4.27 No protein-ligand interaction detected (PLIP) PEG.32: 8 residues within 4Å: Chain B: E.66, R.70, E.178, N.182, W.213, R.215, L.492, L.493 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.70, B:E.178, B:R.215, B:R.215, B:L.493 Water bridges: B:N.182

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

PGE.14: 8 residues within 4Å: Chain A: R.420, D.421, E.422, V.423, H.424 Chain B: R.268, S.271, K.324 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.268, B:R.268, B:K.324, B:K.324, A:R.420, A:V.423, A:H.424, A:H.424 Water bridges: B:S.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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
B

Glucose-6-phosphate 1-dehydrogenase

Related Entries With Identical Sequence