MolNFT v1 · #119393 · protein + DNA

Structure of human tfiid-iia bound to core promoter DNA

5FUR · Tata-box-binding protein: “Structure of human tfiid-iia bound to core promoter DNA”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #119393 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FUR
Type: protein + DNA
Length: 2,412 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tata-box-binding protein; Transcription initiation factor iia subunit 1; Transcription…
EC: 2.3.1.48, 2.7.11.1
UniProt: P20226, P52655, P52657, P21675, Q15545, Q6P1X5, P49848, Q7Z7C8
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 12 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tata-box-binding protein	protein	180	26% helix, 39% strand	P20226
B	Transcription initiation factor iia subunit 1	protein	43	88% helix, 0% strand	P52655
C	Transcription initiation factor iia subunit 1	protein	47	0% helix, 81% strand	P52655
D	Transcription initiation factor iia subunit 2	protein	97	41% helix, 39% strand	P52657
E	Super core promoter	dna	80	—	—
F	Super core promoter	dna	80	—	—
G	Transcription initiation factor tfiid subunit 1 (EC 2.3.1.48, 2.7.11.1)	protein	406	34% helix, 19% strand	P21675
H	Transcription initiation factor tfiid subunit 7	protein	123	20% helix, 42% strand	Q15545
I	Transcription initiation factor tfiid subunit 2	protein	912	37% helix, 18% strand	Q6P1X5
J	Transcription initiation factor tfiid subunit 6	protein	220	80% helix, 0% strand	P49848
K	Transcription initiation factor tfiid subunit 6	protein	198	78% helix, 0% strand	P49848
L	Transcription initiation factor tfiid subunit 8	protein	26	92% helix, 0% strand	Q7Z7C8

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	1068	0.84	0.85	116	empty
2	917	0.78	0.80	94	empty
3	397	0.75	0.85	56	empty
4	1036	0.73	0.77	84	empty
5	373	0.72	0.84	51	empty

Interfaces

21 interfaces between chains.

G–H · 4053 Å² buried · 79 hydrogen bonds · protein-protein
E–F · 3751 Å² buried · 398 hydrogen bonds · nucleic-nucleic
C–D · 1685 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1009 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 860 Å² buried · 11 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified, 1 isopeptide (phosphorylation, isopeptide).

Compared structures

5FUR · Structure of human TFIID-IIA bound to core promoter DNA · the same entry in another collection · chain L against L, 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 P20226
Every structure of UniProt P52655
Every structure of UniProt P52657
Every structure of UniProt P21675
Every structure of UniProt Q15545
Every structure of UniProt Q6P1X5
Every structure of UniProt P49848
Every structure of UniProt Q7Z7C8
Elsewhere: RCSB PDB 5FUR · PDBe 5FUR · UniProt P20226 · UniProt P52655 · UniProt P52657 · UniProt P21675 · UniProt Q15545 · UniProt Q6P1X5 · UniProt P49848 · UniProt Q7Z7C8

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