MolNFT v1 · #30692 · protein

Crystal structure of yoeb under isopropanol condition

2A6S · Toxin yoeb: “Crystal structure of yoeb under isopropanol condition”. X-ray diffraction, 4 pockets (best druggability 0.61). MolNFT v1 #30692 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2A6S
Type: protein
Length: 334 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin yoeb
UniProt: P69348
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Toxin yoeb	protein	83	36% helix, 27% strand	P69348
B, C	Toxin yoeb	protein	84	38% helix, 27% strand	P69348

Ligands and binding sites

IPA · Isopropyl alcohol · additive · 6 copies · chains A, B, C, D

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

Pockets

4 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	193	0.61	0.82	22	empty
2	182	0.54	0.79	23	empty
3	223	0.53	0.77	29	IPA
4	92	0.46	0.80	15	IPA

Interfaces

4 interfaces between chains.

C–D · 707 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 660 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 426 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 34 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2A6S · Crystal structure of YoeB under isopropanol condition · the same entry in another collection · chain A against A, TM-score 1.00
P69348 · AlphaFold monomer V2.0 prediction for toxin yoeb (P69348) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P69348
Elsewhere: RCSB PDB 2A6S · PDBe 2A6S · UniProt P69348

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