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Crystal structure of a transcription factor in complex with ligand

Analyse Crystal structure of a transcription factor in complex with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EQF
Type: protein
Length: 705 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TETR/ACRR family transcriptional regulator
UniProt: A0A4Z1DIH6
Ligands: JB0
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TETR/ACRR family transcriptional regulator	protein	184	74% helix, 0% strand	A0A4Z1DIH6
B	TETR/ACRR family transcriptional regulator	protein	184	72% helix, 0% strand	A0A4Z1DIH6
C	TETR/ACRR family transcriptional regulator	protein	167	75% helix, 0% strand	A0A4Z1DIH6
D	TETR/ACRR family transcriptional regulator	protein	170	74% helix, 0% strand	A0A4Z1DIH6

Ligands and binding sites

JB0 · (6~{R})-3-methyl-8-[(2~{S},4~{R},5~{S},6~{R})-6-methyl-5-[(2~{S},4~{R},5~{R},6~{R})-6-methyl-4-[(2~{S},5~{S}, 6~{S})-6-methyl-5-[(2~{S},4~{R},5~{S},6~{R})-6-methyl-5-[(2~{S},4~{S},5~{S},6~{R})-6-methyl-4-[(2~{S},5~{S}, 6~{S})-6-methyl-5-oxidanyl-oxan-2-yl]oxy-5-oxidanyl-oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-oxan-2-yl]oxy-5-oxidanyl-oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-1,6, 11-tris(oxidanyl)-5,6-dihydrobenzo[a]anthracene-7,12-dione · ligand · 3 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.82	0.82	85	JB0
2	524	0.66	0.77	47	JB0
3	130	0.62	0.86	18	empty
4	144	0.61	0.85	20	empty
5	171	0.58	0.82	22	empty

Interfaces

4 interfaces between chains.

A–B · 1306 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1039 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 194 Å² buried · 1 hydrogen bond · protein-protein
B–D · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

7EQF · Crystal Structure of a Transcription Factor in complex with Ligand · 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 A0A4Z1DIH6
Elsewhere: RCSB PDB 7EQF · PDBe 7EQF · UniProt A0A4Z1DIH6

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