MolNFT v1 · #179256 · protein
Structure of tfiih in TFIIH/RAD4-RAD23-RAD33 DNA opening complex
7K01 · General transcription and DNA repair factor iih subunit TFB1: “Structure of tfiih in TFIIH/RAD4-RAD23-RAD33 DNA opening complex”. Electron microscopy, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #179256 on…
- PDB
- 7K01
- Type
- protein
- Length
- 2,916 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General transcription and DNA repair factor iih subunit TFB1; General transcription and…
- EC
- 3.6.4.12
- UniProt
- P32776, Q12004, Q00578, Q3E7C1, Q02939, P06839, Q04673
- Ligands
- SF4, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | General transcription and DNA repair factor iih subunit TFB1 | protein | 367 | 67% helix, 0% strand | P32776 |
| 4 | General transcription and DNA repair factor iih subunit TFB4 | protein | 284 | 37% helix, 12% strand | Q12004 |
| 7 | DNA repair helicase RAD25 (EC 3.6.4.12) | protein | 634 | 38% helix, 11% strand | Q00578 |
| 5 | RNA polymerase II transcription factor B subunit 5 | protein | 66 | 47% helix, 20% strand | Q3E7C1 |
| 2 | General transcription and DNA repair factor iih subunit TFB2 | protein | 460 | 48% helix, 4% strand | Q02939 |
| 0 | DNA repair helicase RAD3 (EC 3.6.4.12) | protein | 754 | 50% helix, 9% strand | P06839 |
| 6 | General transcription and DNA repair factor iih subunit SSL1 | protein | 351 | 30% helix, 11% strand | Q04673 |
Ligands and binding sites
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.83 | 0.89 | 64 | empty |
| 2 | 1044 | 0.80 | 0.81 | 108 | empty |
| 3 | 787 | 0.79 | 0.83 | 78 | empty |
| 4 | 1017 | 0.79 | 0.80 | 81 | empty |
| 5 | 569 | 0.77 | 0.84 | 92 | empty |
Interfaces
13 interfaces between chains.
- 1–0 · 2649 Ų buried · 32 hydrogen bonds · protein-protein
- 4–6 · 2049 Ų buried · 15 hydrogen bonds · protein-protein
- 1–6 · 1262 Ų buried · 14 hydrogen bonds · protein-protein
- 4–2 · 1030 Ų buried · 8 hydrogen bonds · protein-protein
- 1–4 · 996 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7K01 · Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex · the same entry in another collection · chain 6 against 6, TM-score 1.00
- P06839 · 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 0.97
- Q04673 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 6 against A, TM-score 0.96
- Q12004 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 4 against A, TM-score 0.88
- Q00578 · 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 0.83
- Q02939 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 2 against A, TM-score 0.75
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 P32776
- Every structure of UniProt Q12004
- Every structure of UniProt Q00578
- Every structure of UniProt Q3E7C1
- Every structure of UniProt Q02939
- Every structure of UniProt P06839
- Every structure of UniProt Q04673
- Elsewhere: RCSB PDB 7K01 · PDBe 7K01 · UniProt P32776 · UniProt Q12004 · UniProt Q00578 · UniProt Q3E7C1 · UniProt Q02939 · UniProt P06839 · UniProt Q04673
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