Research workbench

Cryo-EM structure of the human CTP synthase filament

Analyse Cryo-EM structure of the human CTP synthase filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U03
Type: protein
Length: 2,236 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase 1
EC: 6.3.4.2
UniProt: P17812
Ligands: ATP, UTP
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	CTP synthase 1 (EC 6.3.4.2)	protein	559	42% helix, 21% strand	P17812

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.86	0.87	138	ATP, UTP
2	794	0.84	0.87	110	ATP, UTP
3	1055	0.84	0.85	114	ATP, UTP
4	631	0.82	0.87	87	ATP, UTP
5	201	0.82	0.95	27	empty

Interfaces

6 interfaces between chains.

A–C · 1242 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1241 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 709 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 707 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 408 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5U03 · Cryo-EM structure of the human CTP synthase filament · the same entry in another collection · chain A against A, TM-score 1.00
P17812 · AlphaFold monomer V2.0 prediction for CTP synthase 1 (P17812) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P17812
Elsewhere: RCSB PDB 5U03 · PDBe 5U03 · UniProt P17812

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