Research workbench

Tfiid lobe a subcomplex

Analyse Tfiid lobe a subcomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EGF
Type: protein
Length: 1,652 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tata-box-binding protein; Transcription initiation factor tfiid subunit 3; Transcription…
UniProt: P20226, Q5VWG9, O00268, Q15542, P49848, Q16594, Q12962, Q15544, Q16514, Q15543
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 10 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Tata-box-binding protein	protein	177	27% helix, 38% strand	P20226
c	Transcription initiation factor tfiid subunit 3	protein	127	53% helix, 3% strand	Q5VWG9
d	Transcription initiation factor tfiid subunit 4	protein	158	58% helix, 4% strand	O00268
e	Transcription initiation factor tfiid subunit 5	protein	539	19% helix, 26% strand	Q15542
f	Transcription initiation factor tfiid subunit 6	protein	143	35% helix, 12% strand	P49848
i	Transcription initiation factor tfiid subunit 9	protein	121	45% helix, 3% strand	Q16594
j	Transcription initiation factor tfiid subunit 10	protein	95	55% helix, 3% strand	Q12962
k	Transcription initiation factor tfiid subunit 11	protein	98	63% helix, 0% strand	Q15544
l	Transcription initiation factor tfiid subunit 12	protein	107	57% helix, 3% strand	Q16514
m	Transcription initiation factor tfiid subunit 13	protein	87	69% helix, 1% strand	Q15543

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1045	0.86	0.87	96	empty
2	999	0.86	0.87	116	empty
3	945	0.84	0.85	91	empty
4	373	0.78	0.88	57	empty
5	325	0.72	0.85	33	empty

Interfaces

33 interfaces between chains.

c–j · 2630 Å² buried · 13 hydrogen bonds · protein-protein
d–l · 2536 Å² buried · 21 hydrogen bonds · protein-protein
f–i · 2496 Å² buried · 12 hydrogen bonds · protein-protein
k–m · 2414 Å² buried · 13 hydrogen bonds · protein-protein
e–f · 2151 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

7EGF · TFIID lobe A subcomplex · the same entry in another collection · chain m against m, TM-score 1.00
P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain P against A, TM-score 0.98
P49848 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 6… · a predicted model of the same protein · chain f against A, TM-score 0.92

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 P20226
Every structure of UniProt Q5VWG9
Every structure of UniProt O00268
Every structure of UniProt Q15542
Every structure of UniProt P49848
Every structure of UniProt Q16594
Every structure of UniProt Q12962
Every structure of UniProt Q15544
Every structure of UniProt Q16514
Every structure of UniProt Q15543
Elsewhere: RCSB PDB 7EGF · PDBe 7EGF · UniProt P20226 · UniProt Q5VWG9 · UniProt O00268 · UniProt Q15542 · UniProt P49848 · UniProt Q16594 · UniProt Q12962 · UniProt Q15544 · UniProt Q16514 · UniProt Q15543

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