Research workbench

Crystal structure of medicago truncatula ATP-phosphoribosyltransferase in relaxed form

Analyse Crystal structure of medicago truncatula ATP-phosphoribosyltransferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CZL
Type: protein
Length: 2,012 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP phosphoribosyltransferase catalytic subunit
UniProt: G7JFL4
Ligands: CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	ATP phosphoribosyltransferase catalytic subunit	protein	336	30% helix, 28% strand	G7JFL4
C, F	ATP phosphoribosyltransferase catalytic subunit	protein	334	31% helix, 30% strand	G7JFL4

Ligands and binding sites

CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 5 copies · chains B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.85	0.89	83	empty
2	747	0.85	0.89	89	empty
3	1152	0.71	0.75	97	CL
4	971	0.71	0.75	94	CL
5	552	0.63	0.75	48	CL

Interfaces

12 interfaces between chains.

A–E · 1333 Å² buried · 14 hydrogen bonds · protein-protein
C–F · 1318 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1293 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1222 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1188 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6CZL · Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form · the same entry in another collection · 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 G7JFL4
Elsewhere: RCSB PDB 6CZL · PDBe 6CZL · UniProt G7JFL4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.