MolNFT v1 · #137770 · protein

Crystal structure of the wbkc N-formyltransferase (C47S variant) from brucella melitensis

5VYS · GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D…: “Crystal structure of the wbkc N-formyltransferase (C47S variant) from brucella melitensis”. X-ray diffraction, 3 ligands (1YJ, GDP, GMP), 5 pockets (best druggability 0.76).…

PDB: 5VYS
Type: protein
Length: 494 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase
EC: 2.1.2.-, 4.2.1.47
UniProt: F8WJP6
Ligands: 1YJ, GDP, GMP
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase (EC 2.1.2.-, 4.2.1.47)	protein	248	37% helix, 19% strand	F8WJP6
B	GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase (EC 2.1.2.-, 4.2.1.47)	protein	246	34% helix, 20% strand	F8WJP6

Ligands and binding sites

1YJ · N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
GMP · Guanosine · ligand · chains B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	565	0.76	0.83	62	1YJ, GDP, GMP
2	498	0.74	0.82	50	1YJ, GDP
3	78	0.71	0.95	20	empty
4	250	0.56	0.78	36	empty
5	127	0.42	0.76	22	empty

Interfaces

1 interface between chains.

A–B · 1618 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5VYS · Crystal structure of the WbkC N-formyltransferase (C47S variant) from Brucella melitensis · 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 F8WJP6
Elsewhere: RCSB PDB 5VYS · PDBe 5VYS · UniProt F8WJP6

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