MolNFT v1 · #114612 · protein

X-ray structure of wbca from yersinia enterocolitica

5BUV · Putative epimerase: “X-ray structure of wbca from yersinia enterocolitica”. X-ray diffraction, 2 ligands (CYT, PO4), 3 pockets (best druggability 0.77). MolNFT v1 #114612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5BUV
Type: protein
Length: 523 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative epimerase
UniProt: A1JNA0
Ligands: CYT, PO4
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative epimerase	protein	174	5% helix, 45% strand	A1JNA0
B	Putative epimerase	protein	173	5% helix, 43% strand	A1JNA0
C	Putative epimerase	protein	176	6% helix, 44% strand	A1JNA0

Ligands and binding sites

CYT · 6-aminopyrimidin-2(1H)-one · ligand · 2 copies · chains A, C, B
PO4 · Phosphate ion · ion · 5 copies · chains A, C, B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	936	0.77	0.79	73	PO4
2	261	0.67	0.83	30	PO4, CYT
3	127	0.51	0.81	28	empty

Interfaces

2 interfaces between chains.

A–C · 1936 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 271 Å² buried · 4 hydrogen bonds · protein-protein

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 A1JNA0
Elsewhere: RCSB PDB 5BUV · PDBe 5BUV · UniProt A1JNA0

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