MolNFT v1 · #146791 · protein

Lsrb from clostridium saccharobutylicum in complex with ai-2

6DSP · Autoinducer 2-binding protein lsrb: “Lsrb from clostridium saccharobutylicum in complex with ai-2”. X-ray diffraction, 1 ligand (PAV), 5 pockets (best druggability 0.71). MolNFT v1 #146791 on GenesisL1: 3D structure, binding sites…

PDB: 6DSP
Type: protein
Length: 652 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Autoinducer 2-binding protein lsrb
UniProt: U5MRH9
Ligands: PAV
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Autoinducer 2-binding protein lsrb	protein	326	42% helix, 19% strand	U5MRH9

Ligands and binding sites

PAV · (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	343	0.71	0.84	36	empty
2	135	0.50	0.80	26	empty
3	142	0.48	0.78	30	empty
4	67	0.30	0.74	26	empty
5	70	0.29	0.73	27	empty

Interfaces

1 interface between chains.

A–B · 877 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6DSP · LsrB from Clostridium saccharobutylicum in complex with AI-2 · the same entry in another collection · chain A 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 U5MRH9
Elsewhere: RCSB PDB 6DSP · PDBe 6DSP · UniProt U5MRH9

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