MolNFT v1 · #176531 · protein

Structural basis for ligand binding modes of CTP synthase

7DPW: “Structural basis for ligand binding modes of CTP synthase”. Electron microscopy, 2 ligands (CTP, MG), 19 pockets (best druggability 0.87). MolNFT v1 #176531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DPW
Type: protein
Length: 2,224 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase
EC: 6.3.4.2
UniProt: Q9VUL1
Ligands: CTP, MG
Pockets: 19 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	CTP synthase (EC 6.3.4.2)	protein	556	38% helix, 20% strand	Q9VUL1

Ligands and binding sites

CTP · Cytidine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.87	0.88	117	CTP
2	609	0.79	0.84	95	MG, CTP
3	169	0.77	0.93	36	empty
4	187	0.77	0.92	35	empty
5	242	0.75	0.89	48	empty

Interfaces

6 interfaces between chains.

A–C · 1479 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1479 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 592 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 592 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 513 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7DPW · Structural basis for ligand binding modes of CTP synthase · the same entry in another collection · chain A against A, TM-score 1.00
Q9VUL1 · AlphaFold monomer V2.0 prediction for CTP synthase (Q9VUL1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9VUL1
Elsewhere: RCSB PDB 7DPW · PDBe 7DPW · UniProt Q9VUL1

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