SMTL ID : 6rme.1 (1 other biounit)

Structure of IMP bound Plasmodium falciparum IMP-nucleotidase mutant D172N

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-2-1-mer

Ligands

4 x IMP: INOSINIC ACID(Covalent)(Non-covalent)

IMP.1: 16 residues within 4Å: Chain A: D.124, N.126, D.132, T.158, A.159, A.160, S.161, K.259, S.262, F.312, D.317, W.319, D.321, K.325, N.355 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.124, A:N.126, A:N.126, A:T.158, A:A.159, A:S.161, A:K.259, A:S.262, A:D.317, A:N.355 Salt bridges: A:K.325 pi-Stacking: A:W.319, A:W.319, A:W.319 IMP.3: 14 residues within 4Å: Chain B: D.125, N.127, T.159, A.160, A.161, S.162, S.263, F.313, D.318, W.320, D.322, K.326, N.356 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.125, B:A.126, B:N.127, B:N.127, B:T.159, B:A.160, B:S.162, B:S.162, B:S.263, B:D.318, B:N.356 Salt bridges: B:K.326 pi-Stacking: B:W.320, B:W.320, B:W.320 IMP.5: 18 residues within 4Å: Chain C: D.133, A.134, N.135, T.167, A.168, A.169, S.170, K.268, S.271, F.321, G.323, D.326, W.328, D.330, K.334, Q.358, N.364 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:D.133, C:D.133, C:A.134, C:N.135, C:A.168, C:S.170, C:S.271, C:Q.358, C:N.364 Salt bridges: C:K.334 pi-Stacking: C:W.328, C:W.328, C:W.328 IMP.7: 17 residues within 4Å: Chain D: D.125, A.126, N.127, T.159, A.160, A.161, S.162, K.260, S.263, F.313, D.318, W.320, D.322, K.326, Q.350, N.356 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:D.125, D:A.126, D:N.127, D:N.127, D:A.160, D:S.162, D:S.263, D:D.318, D:Q.350, D:N.356 Salt bridges: D:K.326 pi-Stacking: D:W.320, D:W.320, D:W.320

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.124, N.126, D.348, Q.349 Ligands: IMP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.124, A:N.126, A:D.348 MG.4: 5 residues within 4Å: Chain B: D.125, N.127, D.349, Q.350 Ligands: IMP.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.125, B:N.127, B:D.349 MG.6: 5 residues within 4Å: Chain C: D.133, N.135, D.357, Q.358 Ligands: IMP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.133, C:N.135, C:D.357 MG.8: 5 residues within 4Å: Chain D: D.125, N.127, D.349, Q.350 Ligands: IMP.7 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.125, D:N.127, D:D.349, IMP.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain D: Q.171, E.175, E.210, A.211, T.212 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.171, D:E.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carrique, L. et al., Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase. Nat Commun (2020)

Release Date

2020-07-08

Peptides

IMP-specific 5'-nucleotidase, putative: A
IMP-specific 5'-nucleotidase, putative: BD
IMP-specific 5'-nucleotidase, putative: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

IMP-specific 5'-nucleotidase, putative

IMP-specific 5'-nucleotidase, putative

IMP-specific 5'-nucleotidase, putative

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