SMTL ID : 7whs.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 16 residues within 4Å: Chain A: L.14, V.15, G.16, G.17, F.18, G.19, T.20, R.21, K.31, A.60, E.89, G.93, P.97, N.116, S.117, D.118 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.16, A:G.16, A:G.17, A:F.18, A:G.19, A:T.20, A:A.60, A:G.93, A:N.116, A:S.117 Salt bridges: A:R.21, A:R.21, A:K.31, A:K.31, A:E.89 GTP.3: 17 residues within 4Å: Chain B: L.14, V.15, G.16, G.17, F.18, G.19, T.20, R.21, K.31, A.60, E.89, L.92, G.93, P.97, N.116, S.117, D.118 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.16, B:G.16, B:G.17, B:F.18, B:G.19, B:T.20, B:A.60, B:L.92, B:G.93, B:N.116, B:S.117 Salt bridges: B:R.21, B:K.31, B:K.31, B:E.89 GTP.5: 16 residues within 4Å: Chain C: L.14, V.15, G.16, G.17, F.18, G.19, T.20, R.21, K.31, A.60, E.89, G.93, P.97, N.116, S.117, D.118 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.16, C:G.16, C:G.17, C:F.18, C:G.19, C:T.20, C:T.20, C:A.60, C:L.92, C:G.93, C:N.116, C:S.117 Salt bridges: C:R.21, C:R.21, C:K.31, C:K.31, C:E.89 GTP.7: 17 residues within 4Å: Chain D: L.14, V.15, G.16, G.17, F.18, G.19, T.20, R.21, K.31, A.60, E.89, L.92, G.93, P.97, N.116, S.117, D.118 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.16, D:G.16, D:G.17, D:F.18, D:G.19, D:T.20, D:T.20, D:A.60, D:L.92, D:G.93, D:N.116, D:S.117 Salt bridges: D:R.21, D:R.21, D:K.31, D:K.31, D:E.89 GTP.9: 17 residues within 4Å: Chain E: L.14, V.15, G.16, G.17, F.18, G.19, T.20, R.21, K.31, A.60, E.89, L.92, G.93, P.97, N.116, S.117, D.118 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:G.16, E:G.16, E:G.17, E:F.18, E:G.19, E:T.20, E:T.20, E:A.60, E:L.92, E:G.93, E:N.116, E:S.117 Salt bridges: E:R.21, E:K.31, E:K.31, E:E.89 GTP.11: 17 residues within 4Å: Chain F: L.14, V.15, G.16, G.17, F.18, G.19, T.20, R.21, K.31, A.60, E.89, L.92, G.93, P.97, N.116, S.117, D.118 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:G.16, F:G.16, F:G.17, F:F.18, F:G.19, F:T.20, F:A.60, F:L.92, F:G.93, F:N.116, F:S.117 Salt bridges: F:R.21, F:R.21, F:K.31, F:K.31, F:E.89

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.118, D.226 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:D.226, A:D.226 MG.4: 2 residues within 4Å: Chain B: D.118, D.226 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.118, B:D.226, B:D.226 MG.6: 2 residues within 4Å: Chain C: D.118, D.226 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: D.118, D.226 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.118, D:D.226, D:D.226 MG.10: 1 residues within 4Å: Chain E: D.118 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.118 MG.12: 2 residues within 4Å: Chain F: D.118, D.226 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.226, 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

2022-09-21

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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