MolNFT v1 · #170800 · protein

Darb in complex with 3'3'CGAMP

6YJ9 · Cbs domain-containing protein ykul: “Darb in complex with 3'3'CGAMP”. X-ray diffraction, 2 ligands (4BW, CL), 4 pockets (best druggability 0.66). MolNFT v1 #170800 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YJ9
Type: protein
Length: 278 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cbs domain-containing protein ykul
UniProt: O31698
Ligands: 4BW, CL
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cbs domain-containing protein ykul	protein	143	48% helix, 27% strand	O31698
B	Cbs domain-containing protein ykul	protein	135	41% helix, 28% strand	O31698

Ligands and binding sites

4BW · 2-amino-9-[(2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9, 2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one · ligand · 4 copies · chains A, B
CL · Chloride ion · ion · chains A, B

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

Pockets

4 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	657	0.66	0.75	54	4BW, CL
2	81	0.48	0.82	11	empty
3	53	0.36	0.78	12	empty
4	59	0.31	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1474 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6YJ9 · DarB in complex with 3'3'cGAMP · 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 0.96

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 6YJ9 · PDBe 6YJ9 · UniProt O31698

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