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Crystal structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with udp-galacturonic acid and NAD

Analyse Crystal structure of udp-glucuronic acid 4-epimerase from bacillus cereus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZLL
Type: protein
Length: 1,272 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epimerase domain-containing protein
UniProt: J8BY31
Ligands: UGB, NAD
Pockets: 8 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Epimerase domain-containing protein	protein	321	42% helix, 18% strand	J8BY31
B, C	Epimerase domain-containing protein	protein	315	43% helix, 17% strand	J8BY31

Ligands and binding sites

UGB · (2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	515	0.88	0.94	70	UGB, NAD
2	465	0.87	0.94	60	UGB, NAD
3	538	0.87	0.92	84	UGB, NAD
4	491	0.87	0.93	70	UGB, NAD
5	276	0.60	0.79	31	empty

Interfaces

5 interfaces between chains.

A–B · 1350 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1296 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 558 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 136 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 63 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6ZLL · Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with… · the same entry in another collection · chain D against D, 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 J8BY31
Elsewhere: RCSB PDB 6ZLL · PDBe 6ZLL · UniProt J8BY31

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