Research workbench
Structure of the core TFIIH-XPA-DNA complex
Analyse Structure of the core TFIIH-XPA-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RO4
- Type
- protein + DNA
- Length
- 2,396 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA1; DNA2; General transcription and DNA repair factor IIH helicase subunit XPB; General…
- EC
- 3.6.4.12
- UniProt
- P19447, Q6ZYL4, P18074, Q13889, Q13888, Q92759, P23025
- Ligands
- SF4, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.5 · 9 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | DNA1 | dna | 19 | — | — |
| K | DNA2 | dna | 28 | — | — |
| A | General transcription and DNA repair factor IIH helicase subunit XPB (EC 3.6.4.12) | protein | 575 | 29% helix, 15% strand | P19447 |
| F | General transcription factor IIH subunit 5 | protein | 62 | 39% helix, 21% strand | Q6ZYL4 |
| B | TFIIH basal transcription factor complex helicase XPD subunit (EC 3.6.4.12) | protein | 675 | 42% helix, 12% strand | P18074 |
| E | General transcription factor IIH subunit 3 | protein | 237 | 38% helix, 18% strand | Q13889 |
| D | General transcription factor IIH subunit 2 | protein | 280 | 30% helix, 17% strand | Q13888 |
| C | General transcription factor IIH subunit 4 | protein | 386 | 48% helix, 8% strand | Q92759 |
| G | DNA repair protein complementing XP-A cells | protein | 134 | 42% helix, 10% strand | P23025 |
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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.83 | 0.95 | 32 | empty |
| 2 | 1058 | 0.80 | 0.82 | 86 | empty |
| 3 | 1064 | 0.79 | 0.81 | 84 | empty |
| 4 | 253 | 0.76 | 0.89 | 48 | empty |
| 5 | 856 | 0.75 | 0.79 | 95 | empty |
Interfaces
17 interfaces between chains.
- E–D · 2266 Ų buried · 12 hydrogen bonds · protein-protein
- K–B · 1739 Ų buried · 33 hydrogen bonds · protein-nucleic
- E–C · 1148 Ų buried · 12 hydrogen bonds · protein-protein
- F–C · 1055 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1003 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6RO4 · Structure of the core tfiih-xpa-DNA complex · the same entry in another collection · chain K against K, 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 B against A, TM-score 0.98
- Q13889 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 3 (Q13889) · a predicted model of the same protein · chain E against A, TM-score 0.94
- P19447 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P19447
- Every structure of UniProt Q6ZYL4
- Every structure of UniProt P18074
- Every structure of UniProt Q13889
- Every structure of UniProt Q13888
- Every structure of UniProt Q92759
- Every structure of UniProt P23025
- Elsewhere: RCSB PDB 6RO4 · PDBe 6RO4 · UniProt P19447 · UniProt Q6ZYL4 · UniProt P18074 · UniProt Q13889 · UniProt Q13888 · UniProt Q92759 · UniProt P23025
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