MolNFT v1 · #158948 · protein

Structure of the human apo tfiih

6O9M · Tfiih basal transcription factor complex helicase xpd…: “Structure of the human apo tfiih”. Electron microscopy, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #158948 on GenesisL1: 3D structure, binding sites…

PDB: 6O9M
Type: protein
Length: 3,228 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tfiih basal transcription factor complex helicase xpd subunit; General transcription…
EC: 3.6.4.12
UniProt: P18074, P32780, Q92759, P51948, Q13889, Q6ZYL4, Q13888, P19447
Ligands: SF4, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 8 distinct chains · 40% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	Tfiih basal transcription factor complex helicase xpd subunit (EC 3.6.4.12)	protein	732	43% helix, 7% strand	P18074
1	General transcription factor iih subunit 1	protein	433	57% helix, 0% strand	P32780
2	General transcription factor iih subunit 4, P52	protein	453	39% helix, 4% strand	Q92759
3	Cdk-activating kinase assembly factor MAT1	protein	212	53% helix, 3% strand	P51948
4	General transcription factor iih subunit 3	protein	295	29% helix, 9% strand	Q13889
5	General transcription factor iih subunit 5	protein	66	41% helix, 12% strand	Q6ZYL4
6	General transcription factor iih subunit 2	protein	385	31% helix, 14% strand	Q13888
7	Tfiih basal transcription factor complex helicase xpb subunit (EC 3.6.4.12)	protein	652	35% helix, 9% strand	P19447

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 0
ZN · Zinc ion · metal · 6 copies · chains 3, 1, 4, 6

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

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	582	0.88	0.93	104	empty
2	587	0.87	0.93	102	empty
3	654	0.86	0.90	105	empty
4	308	0.84	0.94	63	empty
5	252	0.82	0.95	50	empty

Interfaces

14 interfaces between chains.

0–1 · 3248 Å² buried · 34 hydrogen bonds · protein-protein
1–4 · 2758 Å² buried · 28 hydrogen bonds · protein-protein
4–6 · 2410 Å² buried · 15 hydrogen bonds · protein-protein
1–6 · 2343 Å² buried · 23 hydrogen bonds · protein-protein
2–4 · 1890 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6O9M · Structure of the human apo TFIIH · the same entry in another collection · chain 7 against 7, TM-score 1.00
P18074 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 0 against A, TM-score 0.95
P19447 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 7 against A, TM-score 0.90
Q13888 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 2 (Q13888) · a predicted model of the same protein · chain 6 against A, TM-score 0.87
Q13889 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 3 (Q13889) · a predicted model of the same protein · chain 4 against A, TM-score 0.85

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 P18074
Every structure of UniProt P32780
Every structure of UniProt Q92759
Every structure of UniProt P51948
Every structure of UniProt Q13889
Every structure of UniProt Q6ZYL4
Every structure of UniProt Q13888
Every structure of UniProt P19447
Elsewhere: RCSB PDB 6O9M · PDBe 6O9M · UniProt P18074 · UniProt P32780 · UniProt Q92759 · UniProt P51948 · UniProt Q13889 · UniProt Q6ZYL4 · UniProt Q13888 · UniProt P19447

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