MolNFT v1 · #141219 · protein

ST0452(Y97N)-UTP binding form

5Z09 · Dual sugar-1-phosphate nucleotidylyltransferase: “ST0452(Y97N)-UTP binding form”. X-ray diffraction, 1 ligand (UTP), 20 pockets (best druggability 0.80). MolNFT v1 #141219 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5Z09
Type: protein
Length: 2,337 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual sugar-1-phosphate nucleotidylyltransferase
EC: 2.7.7.-
UniProt: Q975F9
Ligands: UTP
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Dual sugar-1-phosphate nucleotidylyltransferase (EC 2.7.7.-)	protein	401	15% helix, 35% strand	Q975F9
E	Dual sugar-1-phosphate nucleotidylyltransferase (EC 2.7.7.-)	protein	369	11% helix, 36% strand	Q975F9
F	Dual sugar-1-phosphate nucleotidylyltransferase (EC 2.7.7.-)	protein	364	11% helix, 35% strand	Q975F9

Ligands and binding sites

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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.80	0.82	101	UTP
2	692	0.76	0.81	66	UTP
3	597	0.76	0.82	60	UTP
4	734	0.74	0.79	65	UTP
5	605	0.65	0.76	45	empty

Interfaces

8 interfaces between chains.

B–D · 349 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 332 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 311 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 249 Å² buried · 1 hydrogen bond · protein-protein
A–B · 235 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5Z09 · ST0452(Y97N)-UTP binding form · the same entry in another collection · chain F against F, TM-score 1.00
Q975F9 · AlphaFold monomer V2.0 prediction for bifunctional sugar-1-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q975F9
Elsewhere: RCSB PDB 5Z09 · PDBe 5Z09 · UniProt Q975F9

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