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Dcps in complex with covalent inhibitor

Analyse Dcps in complex with covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QDE
Type: protein
Length: 1,156 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: M7GPPPX diphosphatase
EC: 3.6.1.59
UniProt: Q96C86
Ligands: 30S, PO4
Pockets: 16 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	M7GPPPX diphosphatase (EC 3.6.1.59)	protein	287	31% helix, 29% strand	Q96C86
B	M7GPPPX diphosphatase (EC 3.6.1.59)	protein	288	32% helix, 28% strand	Q96C86
C	M7GPPPX diphosphatase (EC 3.6.1.59)	protein	289	32% helix, 28% strand	Q96C86
D	M7GPPPX diphosphatase (EC 3.6.1.59)	protein	292	32% helix, 27% strand	Q96C86

Ligands and binding sites

30S · 2-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid · ligand · 2 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1180	0.84	0.85	88	PO4, 30S
2	1112	0.84	0.85	87	30S, PO4
3	191	0.81	0.95	25	PO4
4	241	0.79	0.92	33	PO4
5	467	0.70	0.80	39	empty

Interfaces

4 interfaces between chains.

A–B · 4758 Å² buried · 84 hydrogen bonds · protein-protein
C–D · 4751 Å² buried · 71 hydrogen bonds · protein-protein
B–D · 668 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 132 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4QDE · Dcps in complex with covalent inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
Q96C86 · AlphaFold monomer V2.0 prediction for M7GPPPX diphosphatase (Q96C86) · a predicted model of the same protein · chain A against A, TM-score 0.81

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 Q96C86
Elsewhere: RCSB PDB 4QDE · PDBe 4QDE · UniProt Q96C86

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