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X-ray structure of pen from bacillus thuringiensis

Analyse X-ray structure of pen from bacillus thuringiensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BWC
Type: protein
Length: 1,936 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polysaccharide biosynthesis protein capd
UniProt: J3UJH9
Ligands: NAP, UD1, SO4
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 6 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polysaccharide biosynthesis protein capd	protein	324	40% helix, 20% strand	J3UJH9
B	Polysaccharide biosynthesis protein capd	protein	316	41% helix, 21% strand	J3UJH9
C	Polysaccharide biosynthesis protein capd	protein	327	41% helix, 20% strand	J3UJH9
D	Polysaccharide biosynthesis protein capd	protein	324	41% helix, 20% strand	J3UJH9
E	Polysaccharide biosynthesis protein capd	protein	322	40% helix, 20% strand	J3UJH9
F	Polysaccharide biosynthesis protein capd	protein	323	41% helix, 20% strand	J3UJH9

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 5 copies · chains A, E, B, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	749	0.89	0.93	73	NAP, UD1
2	1161	0.89	0.90	116	NAP, UD1
3	622	0.89	0.94	67	NAP, UD1
4	747	0.89	0.92	71	NAP, UD1
5	760	0.89	0.92	86	NAP, UD1

Interfaces

12 interfaces between chains.

D–E · 1567 Å² buried · 18 hydrogen bonds · protein-protein
A–F · 1547 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1538 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1266 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1256 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6BWC · X-ray structure of Pen from Bacillus thuringiensis · 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 J3UJH9
Elsewhere: RCSB PDB 6BWC · PDBe 6BWC · UniProt J3UJH9

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