Research workbench

Drae adhesin in complex with bromamphenicol

Analyse Drae adhesin in complex with bromamphenicol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JKL
Type: protein
Length: 833 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dr hemagglutinin structural subunit
UniProt: P24093
Ligands: BRX, CLM, SO4
Pockets: 8 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Dr hemagglutinin structural subunit	protein	139	4% helix, 55% strand	P24093
C, E	Dr hemagglutinin structural subunit	protein	138	4% helix, 54% strand	P24093
F	Dr hemagglutinin structural subunit	protein	140	4% helix, 56% strand	P24093

Ligands and binding sites

BRX · Bromamphenicol · ligand · 8 copies · chains A, B, C, D, F, E
CLM · Chloramphenicol · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D, E

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

Pockets

8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.44	0.79	20	empty
2	92	0.41	0.78	20	empty
3	85	0.41	0.78	20	empty
4	80	0.39	0.78	20	empty
5	78	0.37	0.77	20	empty

Interfaces

6 interfaces between chains.

D–F · 258 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 203 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 196 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 194 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 191 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2JKL · DraE Adhesin in complex with Bromamphenicol · the same entry in another collection · chain F against F, TM-score 1.00
P24093 · AlphaFold monomer V2.0 prediction for dr hemagglutinin structural subunit (P24093) · a predicted model of the same protein · chain B 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 P24093
Elsewhere: RCSB PDB 2JKL · PDBe 2JKL · UniProt P24093

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.