MolNFT v1 · #179259 · protein + DNA
Structure of TFIIH/RAD4-RAD23-RAD33/DNA in DNA opening
7K04 · DNA repair protein RAD33: “Structure of TFIIH/RAD4-RAD23-RAD33/DNA in DNA opening”. Electron microscopy, 3 ligands (SF4, ZN, CA), 20 pockets (best druggability 0.84). MolNFT v1 #179259 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7K04
- Type
- protein + DNA
- Length
- 3,680 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD33; General transcription and DNA repair factor iih subunit TFB2…
- EC
- 3.6.4.12
- UniProt
- Q04231, Q02939, P06839, P32776, Q12004, Q04673, P14736, Q00578, Q3E7C1
- Ligands
- SF4, ZN, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 11 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA repair protein RAD33 | protein | 62 | 48% helix, 3% strand | Q04231 |
| 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 |
| 1 | General transcription and DNA repair factor iih subunit TFB1 | protein | 487 | 56% helix, 7% strand | P32776 |
| 4 | General transcription and DNA repair factor iih subunit TFB4 | protein | 284 | 37% helix, 12% strand | Q12004 |
| 6 | General transcription and DNA repair factor iih subunit SSL1 | protein | 351 | 30% helix, 11% strand | Q04673 |
| Y | Damaged DNA strand | dna | 25 | — | — |
| W | Undamaged DNA strand | dna | 29 | — | — |
| A | DNA repair protein RAD4 | protein | 524 | 40% helix, 19% strand | P14736 |
| 7 | DNA repair helicase RAD25 (EC 3.6.4.12) | protein | 638 | 39% helix, 11% strand | Q00578 |
| 5 | RNA polymerase II transcription factor B subunit 5 | protein | 66 | 42% helix, 17% strand | Q3E7C1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- ZN · Zinc ion · metal · 5 copies · chains 4, 6
- CA · Calcium ion · metal · 2 copies · chains E
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 | 1008 | 0.84 | 0.85 | 128 | empty |
| 2 | 486 | 0.82 | 0.89 | 62 | empty |
| 3 | 1034 | 0.81 | 0.82 | 84 | empty |
| 4 | 773 | 0.81 | 0.84 | 143 | empty |
| 5 | 1043 | 0.80 | 0.81 | 82 | empty |
Interfaces
20 interfaces between chains.
- 0–1 · 2214 Ų buried · 17 hydrogen bonds · protein-protein
- 4–6 · 1623 Ų buried · 4 hydrogen bonds · protein-protein
- 1–4 · 1072 Ų buried · 9 hydrogen bonds · protein-protein
- Y–W · 1067 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- W–A · 1011 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 7K04 · Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening · the same entry in another collection · chain 5 against 5, 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
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 Q04231
- Every structure of UniProt Q02939
- Every structure of UniProt P06839
- Every structure of UniProt P32776
- Every structure of UniProt Q12004
- Every structure of UniProt Q04673
- Every structure of UniProt P14736
- Every structure of UniProt Q00578
- Every structure of UniProt Q3E7C1
- Elsewhere: RCSB PDB 7K04 · PDBe 7K04 · UniProt Q04231 · UniProt Q02939 · UniProt P06839 · UniProt P32776 · UniProt Q12004 · UniProt Q04673 · UniProt P14736 · UniProt Q00578 · UniProt Q3E7C1
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