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Crystal structure of TM0159 with bound imp

Analyse Crystal structure of TM0159 with bound imp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S86
Type: protein
Length: 756 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside-triphosphatase
EC: 3.6.1.15
UniProt: Q9WY06
Ligands: IMP, SO4
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Nucleoside-triphosphatase (EC 3.6.1.15)	protein	189	34% helix, 26% strand	Q9WY06

Ligands and binding sites

IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1136	0.81	0.82	90	empty
2	1142	0.76	0.79	122	IMP, SO4
3	157	0.63	0.86	31	IMP, SO4
4	161	0.62	0.84	30	IMP, SO4
5	75	0.36	0.76	15	empty

Interfaces

4 interfaces between chains.

B–C · 871 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 866 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 714 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 671 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3S86 · Crystal Structure of TM0159 with bound IMP · the same entry in another collection · chain A against A, TM-score 1.00
Q9WY06 · AlphaFold monomer V2.0 prediction for DITP/XTP pyrophosphatase (Q9WY06) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9WY06
Elsewhere: RCSB PDB 3S86 · PDBe 3S86 · UniProt Q9WY06

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