MolNFT v1 · #160426 · protein

Cryoem structure of the substrate-bound human CTP synthase 2 filament

6PK4: “Cryoem structure of the substrate-bound human CTP synthase 2 filament”. Electron microscopy, 2 ligands (UTP, ATP), 20 pockets (best druggability 0.85). MolNFT v1 #160426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PK4
Type: protein
Length: 2,236 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase 2
EC: 6.3.4.2
UniProt: Q9NRF8
Ligands: UTP, ATP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	CTP synthase 2 (EC 6.3.4.2)	protein	559	37% helix, 18% strand	Q9NRF8

Ligands and binding sites

UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
ATP · Adenosine-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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	874	0.85	0.87	83	empty
2	1111	0.84	0.85	87	UTP, ATP
3	1086	0.83	0.84	83	UTP, ATP
4	1131	0.83	0.84	89	UTP, ATP
5	1186	0.83	0.84	88	UTP, ATP

Interfaces

6 interfaces between chains.

A–C · 1499 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1499 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1216 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 1215 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 596 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

6PK4 · cryoEM structure of the substrate-bound human CTP synthase 2 filament · the same entry in another collection · chain A against A, TM-score 1.00
Q9NRF8 · AlphaFold monomer V2.0 prediction for CTP synthase 2 (Q9NRF8) · 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 Q9NRF8
Elsewhere: RCSB PDB 6PK4 · PDBe 6PK4 · UniProt Q9NRF8

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