MolNFT v1 · #146073 · protein

The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 16

6D6N · Transcriptional activator protein lasr: “The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 16”. X-ray diffraction, 2 ligands (FXJ, PHE), 7 pockets (best druggability 0.77). MolNFT v1 #146073 on…

PDB: 6D6N
Type: protein
Length: 625 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional activator protein lasr
UniProt: P25084
Ligands: FXJ, PHE
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional activator protein lasr	protein	160	51% helix, 17% strand	P25084
B	Transcriptional activator protein lasr	protein	152	53% helix, 18% strand	P25084
C	Transcriptional activator protein lasr	protein	160	50% helix, 18% strand	P25084
D	Transcriptional activator protein lasr	protein	153	52% helix, 19% strand	P25084

Ligands and binding sites

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

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

Pockets

7 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	326	0.77	0.88	44	FXJ
2	468	0.75	0.84	61	FXJ
3	435	0.74	0.84	57	FXJ
4	261	0.71	0.85	32	FXJ
5	166	0.43	0.74	21	empty

Interfaces

4 interfaces between chains.

A–C · 942 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 917 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 389 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 149 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6D6N · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 16 · the same entry in another collection · chain D against D, TM-score 1.00
P25084 · AlphaFold monomer V2.0 prediction for transcriptional activator protein lasr (P25084) · a predicted model of the same protein · chain D 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 P25084
Elsewhere: RCSB PDB 6D6N · PDBe 6D6N · UniProt P25084

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