MolNFT v1 · #183596 · protein + DNA
Tfiih in a pre-translocated state (without ADP-BEF3)
7NVW · Tfiih basal transcription factor complex helicase xpd…: “Tfiih in a pre-translocated state (without ADP-BEF3)”. Electron microscopy, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #183596 on GenesisL1: 3D…
- PDB
- 7NVW
- Type
- protein + DNA
- Length
- 2,883 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, ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 13 distinct chains · 47% helix, 12% 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 | 68% 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 | 54% helix, 5% strand | P51948 |
| 4 | General transcription factor iih subunit 3 | protein | 263 | 40% helix, 11% strand | Q13889 |
| 5 | General transcription factor iih subunit 5 | protein | 66 | 45% helix, 24% strand | Q6ZYL4 |
| 6 | General transcription factor iih subunit 2 | protein | 347 | 32% helix, 18% strand | Q13888 |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 605 | 40% helix, 17% strand | P19447 |
| N | Non-template DNA | dna | 21 | — | — |
| T | Template DNA | dna | 21 | — | — |
| W | General transcription factor iie subunit 1 | protein | 15 | 27% helix, 0% strand | P29083 |
| Y | Unassigned peptide, likely xpb | protein | 8 | 0% helix, 25% strand | — |
| Z | Unassigned peptide, likely tfiie-beta | protein | 19 | 16% helix, 0% strand | — |
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 | 181 | 0.80 | 0.96 | 29 | empty |
| 2 | 774 | 0.79 | 0.82 | 95 | empty |
| 3 | 102 | 0.76 | 0.96 | 21 | empty |
| 4 | 66 | 0.72 | 0.97 | 17 | SF4 |
| 5 | 553 | 0.70 | 0.79 | 55 | empty |
Interfaces
21 interfaces between chains.
- 4–6 · 2504 Ų buried · 17 hydrogen bonds · protein-protein
- 1–4 · 2297 Ų buried · 15 hydrogen bonds · protein-protein
- 2–7 · 1464 Ų buried · 14 hydrogen bonds · protein-protein
- 1–6 · 1396 Ų buried · 12 hydrogen bonds · protein-protein
- 2–5 · 1395 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7NVW · TFIIH in a pre-translocated state (without 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 7NVW · PDBe 7NVW · UniProt P18074 · UniProt P32780 · UniProt Q92759 · UniProt P51948 · UniProt Q13889 · UniProt Q6ZYL4 · UniProt Q13888 · UniProt P19447 · UniProt P29083
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