SMTL ID : 7wht.1

Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in complex with GDP-Mannose

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)

GDD.1: 23 residues within 4Å: Chain A: L.14, V.15, G.16, G.17, F.18, G.19, K.31, P.32, P.91, L.92, N.116, S.117, D.118, G.153, V.154, E.169, K.170, N.180, Y.184, E.202, W.224, D.226 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.14, A:G.19, A:K.31, A:K.31, A:N.116, A:N.116, A:S.117, A:S.117, A:V.154, A:E.169, A:N.180, A:E.202, A:E.202 Salt bridges: A:K.31, A:K.170, A:K.170 pi-Cation interactions: A:K.31 GDD.3: 23 residues within 4Å: Chain B: L.14, V.15, G.16, G.17, F.18, G.19, K.31, P.32, P.91, L.92, N.116, S.117, D.118, G.153, V.154, E.169, K.170, N.180, Y.184, E.202, W.224, D.226 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.14, B:G.19, B:K.31, B:K.31, B:N.116, B:N.116, B:S.117, B:V.154, B:E.169, B:N.180, B:E.202, B:E.202 Salt bridges: B:K.31, B:K.170, B:K.170 pi-Cation interactions: B:K.31 GDD.5: 23 residues within 4Å: Chain C: L.14, V.15, G.16, G.17, F.18, G.19, K.31, P.32, P.91, L.92, N.116, S.117, D.118, G.153, V.154, E.169, K.170, N.180, Y.184, E.202, W.224, D.226 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:L.14, C:G.19, C:K.31, C:K.31, C:N.116, C:N.116, C:S.117, C:S.117, C:V.154, C:N.180, C:E.202, C:E.202 Salt bridges: C:K.31, C:K.170, C:K.170 pi-Cation interactions: C:K.31 GDD.7: 23 residues within 4Å: Chain D: L.14, V.15, G.16, G.17, F.18, G.19, K.31, P.32, P.91, L.92, N.116, S.117, D.118, G.153, V.154, E.169, K.170, N.180, Y.184, E.202, W.224, D.226 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:L.14, D:G.19, D:K.31, D:K.31, D:N.116, D:N.116, D:S.117, D:S.117, D:V.154, D:E.169, D:N.180, D:Y.184, D:E.202, D:D.226 Salt bridges: D:K.31, D:K.170, D:K.170 pi-Cation interactions: D:K.31 GDD.9: 23 residues within 4Å: Chain E: L.14, V.15, G.16, G.17, F.18, G.19, K.31, P.32, P.91, L.92, N.116, S.117, D.118, G.153, V.154, E.169, K.170, N.180, Y.184, E.202, W.224, D.226 Ligands: MG.10 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:L.14, E:G.19, E:K.31, E:K.31, E:N.116, E:N.116, E:S.117, E:V.154, E:E.169, E:N.180, E:Y.184, E:E.202 Salt bridges: E:K.31, E:K.170, E:K.170 pi-Cation interactions: E:K.31 GDD.11: 22 residues within 4Å: Chain F: L.14, V.15, G.16, G.17, F.18, G.19, K.31, P.32, P.91, L.92, N.116, S.117, D.118, G.153, V.154, E.169, N.180, Y.184, E.202, W.224, D.226 Ligands: MG.12 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:L.14, F:G.19, F:K.31, F:K.31, F:N.116, F:N.116, F:S.117, F:S.117, F:V.154, F:N.180, F:N.180, F:Y.184, F:E.202, F:D.226 Salt bridges: F:K.31, F:K.170, F:K.170 pi-Cation interactions: F:K.31

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.118, D.226 Ligands: GDD.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.118, A:D.226 MG.4: 3 residues within 4Å: Chain B: D.118, D.226 Ligands: GDD.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.118, B:D.118, B:D.226, B:D.226 MG.6: 3 residues within 4Å: Chain C: D.118, D.226 Ligands: GDD.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.118, C:D.226 MG.8: 3 residues within 4Å: Chain D: D.118, D.226 Ligands: GDD.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.118, D:D.226 MG.10: 3 residues within 4Å: Chain E: D.118, D.226 Ligands: GDD.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.118, E:D.226, E:D.226 MG.12: 3 residues within 4Å: Chain F: D.118, D.226 Ligands: GDD.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.118, F:D.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Structural insights into selective inhibition of leishmanial GDP-mannose pyrophosphorylase. Cell Discov (2022)

Release Date

2022-10-12

Peptides

Nucleotidyl transferase family protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleotidyl transferase family protein

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