MolNFT v1 · #107545 · protein

Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 ångström in complex with N-acetylglucosamine and inorganic phosphate

4UDG · UHGB_MP: “Crystal structure of B-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 ångström in complex with…”. X-ray diffraction, 3 ligands (NDG, K, PO4), 20 pockets (best druggability 0.78). MolNFT v1 #107545 on GenesisL1: 3D…

PDB: 4UDG
Type: protein
Length: 1,922 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UHGB_MP
EC: 2.4.1.-
UniProt: D9ZDQ9
Ligands: NDG, K, PO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	UHGB_MP (EC 2.4.1.-)	protein	320	7% helix, 49% strand	D9ZDQ9
B, E	UHGB_MP (EC 2.4.1.-)	protein	321	5% helix, 50% strand	D9ZDQ9

Ligands and binding sites

NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains A, C, B, D, F, E
K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 7 copies · chains A, C, B, D, F, E
EDO · 1,2-ethanediol · additive · 5 copies · chains A, 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	360	0.78	0.88	38	PO4, NDG, GOL
2	353	0.78	0.88	38	PO4, NDG, GOL
3	353	0.78	0.88	35	PO4, NDG, GOL
4	371	0.78	0.87	41	PO4, NDG, GOL
5	350	0.78	0.88	38	PO4, NDG, GOL

Interfaces

9 interfaces between chains.

A–E · 1304 Å² buried · 16 hydrogen bonds · protein-protein
C–F · 1303 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1290 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 878 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 877 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4UDG · Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in… · the same entry in another collection · chain A 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 D9ZDQ9
Elsewhere: RCSB PDB 4UDG · PDBe 4UDG · UniProt D9ZDQ9

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