MolNFT v1 · #160429 · protein

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

6PK7: “Cryoem structure of the product-bound human CTP synthase 2 filament”. Electron microscopy, 2 ligands (ADP, CTP), 20 pockets (best druggability 0.86). MolNFT v1 #160429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PK7
Type: protein
Length: 2,228 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: ADP, CTP
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	CTP synthase 2 (EC 6.3.4.2)	protein	557	36% helix, 19% strand	Q9NRF8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, D, E, F
CTP · Cytidine-5'-triphosphate · ligand · 4 copies · chains A, 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.86	0.87	50	empty
2	953	0.77	0.80	75	ADP, CTP
3	1044	0.77	0.79	87	ADP, CTP
4	1034	0.77	0.79	77	ADP, CTP
5	1045	0.77	0.79	88	ADP, CTP

Interfaces

6 interfaces between chains.

D–F · 1490 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 1490 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 865 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 865 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 672 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

6PK7 · cryoEM structure of the product-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 6PK7 · PDBe 6PK7 · UniProt Q9NRF8

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