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The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 14

Analyse The structure of ligand binding domain of lasr in complex with tp-1 homolog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6D6L
Type: protein
Length: 660 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional activator protein lasr
UniProt: P25084
Ligands: FY4
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional activator protein lasr	protein	165	48% helix, 18% strand	P25084
B	Transcriptional activator protein lasr	protein	163	52% helix, 18% strand	P25084
C, D	Transcriptional activator protein lasr	protein	166	55% helix, 16% strand	P25084

Ligands and binding sites

FY4 · 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl) amino]methyl}phenyl 4-chlorobenzoate · ligand · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	277	0.78	0.90	37	FY4
2	283	0.78	0.89	34	FY4
3	292	0.76	0.88	38	FY4
4	470	0.75	0.84	58	FY4
5	173	0.47	0.76	32	empty

Interfaces

4 interfaces between chains.

C–D · 931 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 923 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 362 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 282 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6D6L · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14 · the same entry in another collection · chain A against A, TM-score 1.00
P25084 · AlphaFold monomer V2.0 prediction for transcriptional activator protein lasr (P25084) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P25084
Elsewhere: RCSB PDB 6D6L · PDBe 6D6L · UniProt P25084

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