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Crystal structure of plasmodium falciparum pnp with 5'-methylthio- immucillin-H

Analyse Crystal structure of plasmodium falciparum pnp with 5'-methylthio- immucillin-H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q1G
Type: protein
Length: 1,458 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uridine phosphorylase putative
EC: 2.4.2.1
UniProt: Q8I3X4
Ligands: MTI, SO4
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Uridine phosphorylase putative (EC 2.4.2.1)	protein	243	34% helix, 30% strand	Q8I3X4

Ligands and binding sites

MTI · 3,4-dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 22 copies · chains A, B, F, C, D, E
IPA · Isopropyl alcohol · additive · 9 copies · chains A, B, F, C, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	374	0.79	0.88	55	SO4, MTI
2	369	0.79	0.88	54	SO4, MTI
3	356	0.78	0.88	52	SO4, MTI
4	325	0.77	0.88	46	SO4, MTI
5	363	0.77	0.87	57	SO4, MTI

Interfaces

12 interfaces between chains.

C–D · 2097 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2038 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2030 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1273 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 1262 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1Q1G · Crystal structure of Plasmodium falciparum PNP with 5'-methylthio-immucillin-H · the same entry in another collection · chain C against C, TM-score 1.00
Q8I3X4 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (Q8I3X4) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8I3X4
Elsewhere: RCSB PDB 1Q1G · PDBe 1Q1G · UniProt Q8I3X4

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