MolNFT v1 · #122656 · protein + DNA
Human core tfiih bound to DNA within the pic
5IVW · Tfiih basal transcription factor complex helicase xpb…: “Human core tfiih bound to DNA within the pic”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #122656 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IVW
- Type
- protein + DNA
- Length
- 1,896 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tfiih basal transcription factor complex helicase xpb subunit; Tfiih basal transcription…
- EC
- 3.6.4.12
- UniProt
- P19447, P18074, Q13888, Q6ZYL4, Q92759, Q13889
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Tfiih basal transcription factor complex helicase xpb subunit (EC 3.6.4.12) | protein | 475 | 35% helix, 17% strand | P19447 |
| W | Tfiih basal transcription factor complex helicase xpd subunit (EC 3.6.4.12) | protein | 665 | 48% helix, 11% strand | P18074 |
| 0 | General transcription factor iih subunit 2 | protein | 188 | 43% helix, 25% strand | Q13888 |
| 1 | General transcription factor iih subunit 5 | protein | 62 | 31% helix, 26% strand | Q6ZYL4 |
| 2 | General transcription factor iih subunit 4 | protein | 274 | 66% helix, 5% strand | Q92759 |
| 3 | General transcription factor iih subunit 3 | protein | 193 | 52% helix, 21% strand | Q13889 |
| X | Scp-X | dna | 19 | — | — |
| Y | Scp-Y | dna | 20 | — | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.84 | 0.85 | 77 | empty |
| 2 | 772 | 0.81 | 0.84 | 99 | empty |
| 3 | 770 | 0.77 | 0.81 | 88 | empty |
| 4 | 736 | 0.75 | 0.80 | 88 | empty |
| 5 | 187 | 0.72 | 0.89 | 40 | empty |
Interfaces
10 interfaces between chains.
- 1–2 · 1037 Ų buried · 21 hydrogen bonds · protein-protein
- X–Y · 927 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- 2–3 · 696 Ų buried · 16 hydrogen bonds · protein-protein
- W–0 · 606 Ų buried · 5 hydrogen bonds · protein-protein
- V–1 · 573 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5IVW · Human core TFIIH bound to DNA within the PIC · the same entry in another collection · chain 1 against 1, TM-score 1.00
- Q13888 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 2 (Q13888) · a predicted model of the same protein · chain 0 against A, TM-score 0.95
- Q13889 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 3 (Q13889) · a predicted model of the same protein · chain 3 against A, TM-score 0.92
- P18074 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain W against A, TM-score 0.82
- P19447 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain V against A, TM-score 0.78
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 P18074
- Every structure of UniProt Q13888
- Every structure of UniProt Q6ZYL4
- Every structure of UniProt Q92759
- Every structure of UniProt Q13889
- Elsewhere: RCSB PDB 5IVW · PDBe 5IVW · UniProt P19447 · UniProt P18074 · UniProt Q13888 · UniProt Q6ZYL4 · UniProt Q92759 · UniProt Q13889
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