MolNFT v1 · #135581 · protein

Cryoem structure of the CTP synthase filament at 4.6 ångström resolution

5U3C: “Cryoem structure of the CTP synthase filament at 4.6 ångström resolution”. Electron microscopy, 2 ligands (CTP, ADP), 20 pockets (best druggability 0.89). MolNFT v1 #135581 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5U3C
Type: protein
Length: 2,136 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase
EC: 6.3.4.2
UniProt: B7MLA1
Ligands: CTP, ADP
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	CTP synthase (EC 6.3.4.2)	protein	534	41% helix, 23% strand	B7MLA1

Ligands and binding sites

CTP · Cytidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, C, B, 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	933	0.89	0.91	116	CTP
2	101	0.76	0.96	28	empty
3	85	0.74	0.96	31	empty
4	263	0.70	0.85	51	empty
5	248	0.68	0.84	49	ADP

Interfaces

6 interfaces between chains.

A–B · 1186 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1176 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 740 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 732 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 607 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5U3C · CryoEM structure of the CTP synthase filament at 4.6 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
B7MLA1 · AlphaFold monomer V2.0 prediction for CTP synthase (B7MLA1) · 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 B7MLA1
Elsewhere: RCSB PDB 5U3C · PDBe 5U3C · UniProt B7MLA1

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