MolNFT v1 · #172777 · protein + DNA
Core tfiih-xpa-DNA complex with modelled P62 subunit
7AD8 · DNA (49-mer): “Core tfiih-xpa-DNA complex with modelled P62 subunit”. Electron microscopy, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #172777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7AD8
- Type
- protein + DNA
- Length
- 2,602 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (49-mer); General transcription and DNA repair factor iih helicase subunit xpb…
- EC
- 3.6.4.12
- UniProt
- P19447, Q6ZYL4, P18074, Q13889, Q13888, Q92759, P23025, P32780
- Ligands
- SF4, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | DNA (49-mer) | dna | 19 | — | — |
| K | DNA (49-mer) | dna | 28 | — | — |
| A | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 575 | 31% helix, 16% strand | P19447 |
| F | General transcription factor iih subunit 5 | protein | 62 | 34% helix, 21% strand | Q6ZYL4 |
| B | Tfiih basal transcription factor complex helicase xpd subunit (EC 3.6.4.12) | protein | 675 | 41% helix, 12% strand | P18074 |
| E | General transcription factor iih subunit 3 | protein | 237 | 35% helix, 18% strand | Q13889 |
| D | General transcription factor iih subunit 2 | protein | 280 | 27% helix, 16% strand | Q13888 |
| C | General transcription factor iih subunit 4 | protein | 386 | 48% helix, 7% strand | Q92759 |
| G | DNA repair protein complementing xp-a cells | protein | 134 | 40% helix, 7% strand | P23025 |
| I | General transcription factor iih subunit 1 | protein | 206 | 58% helix, 0% strand | P32780 |
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 | 286 | 0.84 | 0.95 | 35 | empty |
| 2 | 1120 | 0.79 | 0.81 | 91 | empty |
| 3 | 231 | 0.76 | 0.90 | 44 | empty |
| 4 | 107 | 0.74 | 0.95 | 20 | SF4 |
| 5 | 420 | 0.73 | 0.83 | 41 | empty |
Interfaces
21 interfaces between chains.
- E–D · 2323 Ų buried · 14 hydrogen bonds · protein-protein
- K–B · 1751 Ų buried · 26 hydrogen bonds · protein-nucleic
- E–I · 1395 Ų buried · 3 hydrogen bonds · protein-protein
- E–C · 1156 Ų buried · 12 hydrogen bonds · protein-protein
- F–C · 1099 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7AD8 · Core TFIIH-XPA-DNA complex with modelled p62 subunit · the same entry in another collection · chain I against I, 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
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
- Every structure of UniProt P32780
- Elsewhere: RCSB PDB 7AD8 · PDBe 7AD8 · UniProt P19447 · UniProt Q6ZYL4 · UniProt P18074 · UniProt Q13889 · UniProt Q13888 · UniProt Q92759 · UniProt P23025 · UniProt P32780
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