MolNFT v1 · #30691 · protein

Crystal structure of yoeb under peg condition

2A6R · Toxin yoeb: “Crystal structure of yoeb under peg condition”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.60). MolNFT v1 #30691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2A6R
Type: protein
Length: 503 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin yoeb
UniProt: P69348
Ligands: MG
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F	Toxin yoeb	protein	84	36% helix, 26% strand	P69348
C	Toxin yoeb	protein	83	35% helix, 27% strand	P69348

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	475	0.60	0.75	58	empty
2	130	0.43	0.76	29	empty

Interfaces

6 interfaces between chains.

A–B · 689 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 684 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 674 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 248 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 176 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2A6R · Crystal structure of YoeB under PEG condition · the same entry in another collection · chain F against F, 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 0.98

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 2A6R · PDBe 2A6R · UniProt P69348

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