MolNFT v1 · #136936 · protein

Lytr-CSP2A-psr enzyme from actinomyces oris

5V8C · Transcriptional regulator: “Lytr-CSP2A-psr enzyme from actinomyces oris”. X-ray diffraction, 2 ligands (CO, PO4), 3 pockets (best druggability 0.82). MolNFT v1 #136936 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V8C
Type: protein
Length: 272 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator
UniProt: A0A0X8K2V1
Ligands: CO, PO4
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator	protein	272	39% helix, 24% strand	A0A0X8K2V1

Ligands and binding sites

CO · Cobalt (II) ion · metal · chains A
PO4 · Phosphate ion · ion · chains A
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	547	0.82	0.87	47	PE4
2	106	0.58	0.85	22	empty
3	68	0.44	0.82	21	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5V8C · LytR-Csp2A-Psr enzyme from Actinomyces oris · 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 A0A0X8K2V1
Elsewhere: RCSB PDB 5V8C · PDBe 5V8C · UniProt A0A0X8K2V1

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