MolNFT v1 · #141220 · protein

ST0452(Y97N)-glcnac binding form

5Z0A · Dual sugar-1-phosphate nucleotidylyltransferase: “ST0452(Y97N)-glcnac binding form”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.77). MolNFT v1 #141220 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5Z0A
Type: protein
Length: 2,392 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: NAG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F	Dual sugar-1-phosphate nucleotidylyltransferase (EC 2.7.7.-)	protein	400	19% helix, 36% strand	Q975F9
C	Dual sugar-1-phosphate nucleotidylyltransferase (EC 2.7.7.-)	protein	396	19% helix, 36% strand	Q975F9
E	Dual sugar-1-phosphate nucleotidylyltransferase (EC 2.7.7.-)	protein	396	18% helix, 36% strand	Q975F9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1155	0.77	0.79	95	empty
2	591	0.76	0.83	50	NAG
3	753	0.76	0.80	73	empty
4	794	0.76	0.80	76	empty
5	562	0.75	0.82	53	empty

Interfaces

7 interfaces between chains.

C–E · 865 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 839 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 834 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 350 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 327 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5Z0A · ST0452(Y97N)-GlcNAc 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 C against A, TM-score 1.00

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 5Z0A · PDBe 5Z0A · UniProt Q975F9

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