MolNFT v1 · #183597 · protein + DNA
Tfiih in a post-translocated state (with ADP-BEF3)
7NVX · Tfiih basal transcription factor complex helicase xpd…: “Tfiih in a post-translocated state (with ADP-BEF3)”. Electron microscopy, 5 ligands (SF4, ADP, BEF), 20 pockets (best druggability 0.82). MolNFT v1 #183597 on GenesisL1: 3D…
- PDB
- 7NVX
- Type
- protein + DNA
- Length
- 2,870 residues
- Chains
- 13
- 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, P29083
- Ligands
- SF4, ADP, BEF, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 13 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Tfiih basal transcription factor complex helicase xpd subunit (EC 3.6.4.12) | protein | 714 | 50% helix, 11% strand | P18074 |
| 1 | General transcription factor iih subunit 1 | protein | 265 | 67% helix, 0% strand | P32780 |
| 2 | General transcription factor iih subunit 4 | protein | 390 | 55% helix, 12% strand | Q92759 |
| 3 | Cdk-activating kinase assembly factor MAT1 | protein | 149 | 53% helix, 4% strand | P51948 |
| 4 | General transcription factor iih subunit 3 | protein | 263 | 40% helix, 12% strand | Q13889 |
| 5 | General transcription factor iih subunit 5 | protein | 66 | 41% helix, 24% strand | Q6ZYL4 |
| 6 | General transcription factor iih subunit 2 | protein | 329 | 31% helix, 17% strand | Q13888 |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 605 | 40% helix, 18% strand | P19447 |
| N | Non-template DNA | dna | 25 | — | — |
| T | Template DNA | dna | 25 | — | — |
| W | General transcription factor iie subunit 1 | protein | 15 | 27% helix, 0% strand | P29083 |
| Y | Unassigned peptide, likely xpb | protein | 8 | 0% helix, 13% strand | — |
| Z | Unassigned peptide, likely tfiie-beta | protein | 16 | 0% helix, 0% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- ADP · Adenosine-5'-diphosphate · ligand · chains 7
- BEF · Beryllium trifluoride ion · ligand · chains 7
- ZN · Zinc ion · metal · 7 copies · chains 3, 4, 6
- MG · Magnesium ion · metal · chains 7
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 | 228 | 0.82 | 0.95 | 26 | empty |
| 2 | 825 | 0.79 | 0.82 | 99 | empty |
| 3 | 154 | 0.75 | 0.93 | 27 | empty |
| 4 | 227 | 0.71 | 0.87 | 38 | empty |
| 5 | 58 | 0.70 | 0.97 | 19 | SF4 |
Interfaces
20 interfaces between chains.
- 4–6 · 2432 Ų buried · 22 hydrogen bonds · protein-protein
- 1–4 · 2345 Ų buried · 16 hydrogen bonds · protein-protein
- 1–6 · 1510 Ų buried · 9 hydrogen bonds · protein-protein
- 2–7 · 1404 Ų buried · 14 hydrogen bonds · protein-protein
- 2–5 · 1295 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7NVX · TFIIH in a post-translocated state (with ADP-BeF3) · the same entry in another collection · chain Z against Z, TM-score 1.00
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
- Every structure of UniProt P29083
- Elsewhere: RCSB PDB 7NVX · PDBe 7NVX · UniProt P18074 · UniProt P32780 · UniProt Q92759 · UniProt P51948 · UniProt Q13889 · UniProt Q6ZYL4 · UniProt Q13888 · UniProt P19447 · UniProt P29083
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