MolNFT v1 · #139068 · protein

Crystal structure of the smcr complexed with qstatin

5X3R · Luxr family transcriptional regulator: “Crystal structure of the smcr complexed with qstatin”. X-ray diffraction, 2 ligands (7Y3, SO4), 11 pockets (best druggability 0.77). MolNFT v1 #139068 on GenesisL1: 3D structure, binding sites…

PDB: 5X3R
Type: protein
Length: 805 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Luxr family transcriptional regulator
UniProt: Q9L8G8
Ligands: 7Y3, SO4
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Luxr family transcriptional regulator	protein	203	68% helix, 1% strand	Q9L8G8
B	Luxr family transcriptional regulator	protein	202	70% helix, 1% strand	Q9L8G8
C	Luxr family transcriptional regulator	protein	200	69% helix, 1% strand	Q9L8G8
D	Luxr family transcriptional regulator	protein	200	71% helix, 1% strand	Q9L8G8

Ligands and binding sites

7Y3 · 1-(5-bromanylthiophen-2-yl)sulfonylpyrazole · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	481	0.77	0.85	49	empty
2	237	0.75	0.89	41	7Y3
3	359	0.74	0.85	46	SO4
4	301	0.72	0.85	39	7Y3
5	259	0.71	0.86	42	7Y3

Interfaces

5 interfaces between chains.

B–C · 1623 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1532 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 457 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 217 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 214 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 modified, 3 disulfide (engineered, disulfide).

Compared structures

5X3R · Crystal structure of the SmcR complexed with QStatin · 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 Q9L8G8
Elsewhere: RCSB PDB 5X3R · PDBe 5X3R · UniProt Q9L8G8

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