Research workbench

Human tfiid bound to promoter DNA and tfiia

Analyse Human tfiid bound to promoter DNA and tfiia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MZM
Type: protein + DNA
Length: 3,960 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription initiation factor tfiid subunit 1, TAF1; Transcription initiation factor…
UniProt: Q6P1X5, O00268, Q15542, P49848, Q15545, Q7Z7C8, Q16594, Q12962, Q16514, P20226, P52657
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 17 distinct chains · 43% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription initiation factor tfiid subunit 1, TAF1	protein	445	38% helix, 16% strand	—
B	Transcription initiation factor tfiid subunit 2, TAF2	protein	968	37% helix, 14% strand	Q6P1X5
D	Transcription initiation factor tfiid subunit 4, TAF4	protein	128	77% helix, 1% strand	O00268
G	Transcription initiation factor tfiid subunit 5,TAF5	protein	473	22% helix, 26% strand	Q15542
H	Transcription initiation factor tfiid subunit 6	protein	257	74% helix, 0% strand	P49848
I	Transcription initiation factor tfiid subunit 6	protein	339	67% helix, 0% strand	P49848
J	Transcription initiation factor tfiid subunit 7	protein	123	18% helix, 42% strand	Q15545
K	Transcription initiation factor tfiid subunit 8, TAF8	protein	202	48% helix, 1% strand	Q7Z7C8
L	Transcription initiation factor tfiid subunit 9, TAF9	protein	104	64% helix, 0% strand	Q16594
O	Transcription initiation factor tfiid subunit 10	protein	82	63% helix, 1% strand	Q12962
R	Transcription initiation factor tfiid subunit 12	protein	74	66% helix, 1% strand	Q16514
T	Tata-box-binding protein	protein	180	27% helix, 41% strand	P20226
U	Scp DNA (80-mer)	dna	80	—	—
V	Scp DNA (80-mer)	dna	80	—	—
W	Transcription initiation factor iia subunit 1	protein	90	41% helix, 42% strand	—
X	Transcription initiation factor iia subunit 2	protein	97	40% helix, 41% strand	P52657
Z	Unk	protein	238	29% helix, 1% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.88	0.89	124	empty
2	1189	0.81	0.82	125	empty
3	604	0.81	0.86	63	empty
4	1059	0.79	0.80	121	empty
5	821	0.77	0.81	87	empty

Interfaces

47 interfaces between chains.

A–J · 3968 Å² buried · 60 hydrogen bonds · protein-protein
U–V · 3679 Å² buried · 301 hydrogen bonds · nucleic-nucleic
W–X · 2652 Å² buried · 39 hydrogen bonds · protein-protein
K–O · 2451 Å² buried · 18 hydrogen bonds · protein-protein
B–K · 2276 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6MZM · Human TFIID bound to promoter DNA and TFIIA · the same entry in another collection · chain R against R, 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 Q6P1X5
Every structure of UniProt O00268
Every structure of UniProt Q15542
Every structure of UniProt P49848
Every structure of UniProt Q15545
Every structure of UniProt Q7Z7C8
Every structure of UniProt Q16594
Every structure of UniProt Q12962
Every structure of UniProt Q16514
Every structure of UniProt P20226
Every structure of UniProt P52657
Elsewhere: RCSB PDB 6MZM · PDBe 6MZM · UniProt Q6P1X5 · UniProt O00268 · UniProt Q15542 · UniProt P49848 · UniProt Q15545 · UniProt Q7Z7C8 · UniProt Q16594 · UniProt Q12962 · UniProt Q16514 · UniProt P20226 · UniProt P52657

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