MolNFT v1 · #170799 · protein

DARB-APO

6YJ8 · Cbs domain-containing protein ykul: “DARB-APO”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #170799 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YJ8
Type: protein
Length: 275 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cbs domain-containing protein ykul
UniProt: O31698
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cbs domain-containing protein ykul	protein	142	41% helix, 26% strand	O31698
B	Cbs domain-containing protein ykul	protein	133	37% helix, 28% strand	O31698

Ligands and binding sites

ACT · Acetate ion · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains B

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	578	0.65	0.75	43	ACT, PEG
2	72	0.45	0.81	12	empty

Interfaces

1 interface between chains.

A–B · 1419 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6YJ8 · DarB-APO · the same entry in another collection · chain A against A, TM-score 1.00
O31698 · AlphaFold monomer V2.0 prediction for cbs domain-containing protein ykul (O31698) · a predicted model of the same protein · chain B 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 O31698
Elsewhere: RCSB PDB 6YJ8 · PDBe 6YJ8 · UniProt O31698

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