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Ribb from vibrio cholera bound with D-xylulose-5-phosphate (D-XY5P) and manganese

Analyse Ribb from vibrio cholera bound with D-xylulose-5-phosphate (D-XY5P) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7UF2
Type: protein
Length: 209 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3,4-dihydroxy-2-butanone 4-phosphate synthase
EC: 4.1.99.12
UniProt: A0A0H6NPW4
Ligands: 5SP, MN
Pockets: 1 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12)	protein	209	43% helix, 21% strand	A0A0H6NPW4

Ligands and binding sites

5SP · 5-O-phosphono-D-xylulose · ligand · chains A
MN · Manganese (II) ion · metal · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.42	0.82	15	5SP, MN

Compared structures

7UF2 · RibB from Vibrio cholera bound with D-xylulose-5-phosphate (D-Xy5P) and manganese · 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 A0A0H6NPW4
Elsewhere: RCSB PDB 7UF2 · PDBe 7UF2 · UniProt A0A0H6NPW4

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