MolNFT v1 · #118310 · protein

Crystal structure of cody from bacillus cereus

5EY2 · GTP-sensing transcriptional pleiotropic repressor cody: “Crystal structure of cody from bacillus cereus”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #118310 on GenesisL1: 3D structure, binding sites and…

PDB: 5EY2
Type: protein
Length: 965 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-sensing transcriptional pleiotropic repressor cody
UniProt: Q819X8
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTP-sensing transcriptional pleiotropic repressor cody	protein	254	47% helix, 18% strand	Q819X8
D	GTP-sensing transcriptional pleiotropic repressor cody	protein	226	45% helix, 14% strand	Q819X8
C	GTP-sensing transcriptional pleiotropic repressor cody	protein	231	44% helix, 17% strand	Q819X8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.78	0.90	48	empty
2	916	0.77	0.80	112	empty
3	196	0.70	0.87	34	empty
4	114	0.65	0.88	24	empty
5	239	0.54	0.76	29	empty

Interfaces

6 interfaces between chains.

A–B · 1344 Å² buried · 11 hydrogen bonds · protein-protein
D–C · 1246 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 1008 Å² buried · 1 hydrogen bond · protein-protein
B–C · 842 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 712 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 29 modified (engineered).

Compared structures

5EY2 · Crystal structure of CodY from Bacillus cereus · the same entry in another collection · chain C against C, TM-score 1.00
Q819X8 · AlphaFold monomer V2.0 prediction for GTP-sensing transcriptional pleiotropic repressor… · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q819X8
Elsewhere: RCSB PDB 5EY2 · PDBe 5EY2 · UniProt Q819X8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.