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

Structure of N-terminal truncated IMP bound Plasmodium falciparum IMP-nucleotidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-tetramer

Ligands

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

IMP.1: 17 residues within 4Å: Chain A: D.140, N.142, D.148, T.174, A.175, A.176, S.177, K.275, S.278, F.328, D.333, W.335, D.337, K.341, Q.365, N.371 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.140, A:N.142, A:N.142, A:T.174, A:A.175, A:S.177, A:K.275, A:S.278, A:D.333, A:Q.365, A:N.371 Salt bridges: A:K.341 pi-Stacking: A:W.335, A:W.335, A:W.335 IMP.3: 15 residues within 4Å: Chain B: D.140, N.142, T.174, A.175, A.176, S.177, S.278, F.328, G.330, D.333, W.335, D.337, K.341, N.371 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.140, B:D.140, B:N.142, B:T.174, B:A.175, B:S.177, B:S.177, B:S.278, B:D.333, B:N.371 Salt bridges: B:K.341 pi-Stacking: B:W.335, B:W.335, B:W.335 IMP.5: 17 residues within 4Å: Chain C: D.140, N.142, T.174, A.175, A.176, S.177, K.275, S.278, F.328, G.330, D.333, W.335, D.337, K.341, Q.365, N.371 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:D.140, C:D.140, C:A.141, C:N.142, C:A.175, C:S.177, C:S.177, C:S.278, C:N.371 Salt bridges: C:K.341 pi-Stacking: C:W.335, C:W.335, C:W.335 IMP.7: 16 residues within 4Å: Chain D: D.140, N.142, T.174, A.175, S.177, K.275, S.278, F.328, D.333, W.335, D.337, K.341, D.364, Q.365, N.371 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.142, D:A.175, D:S.177, D:S.177, D:S.177, D:S.278, D:D.333 Salt bridges: D:K.341 pi-Stacking: D:W.335, D:W.335, D:W.335

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.140, N.142, D.364, Q.365 Ligands: IMP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.140, A:N.142, A:D.364 MG.4: 6 residues within 4Å: Chain B: D.140, N.142, E.143, D.364, Q.365 Ligands: IMP.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.140, B:N.142, B:D.364 MG.6: 5 residues within 4Å: Chain C: D.140, N.142, D.364, Q.365 Ligands: IMP.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.140, C:D.140, C:N.142, C:D.364 MG.8: 5 residues within 4Å: Chain D: D.140, N.142, D.364, Q.365 Ligands: IMP.7 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.140, D:N.142, D:D.364, IMP.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain D: Q.186, E.190, E.225, A.226, T.227 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.186, D:E.225

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

2020-07-15

Peptides

IMP-specific 5'-nucleotidase, putative: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

IMP-specific 5'-nucleotidase, putative

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