Research workbench
Cryo-EM structure of the human tfiih core complex
Analyse Cryo-EM structure of the human tfiih core complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NMI
- Type
- protein
- Length
- 3,178 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General transcription and DNA repair factor iih helicase subunit xpb; General…
- EC
- 3.6.4.12
- UniProt
- Q92759, Q13889, Q6ZYL4, P51948
- Ligands
- SF4, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 8 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 653 | 37% helix, 17% strand | — |
| B | General transcription and DNA repair factor iih helicase subunit xpd | protein | 760 | 44% helix, 12% strand | — |
| C | General transcription factor iih subunit 1, P62 | protein | 408 | 52% helix, 0% strand | — |
| D | General transcription factor iih subunit 4, P52 | protein | 452 | 43% helix, 12% strand | Q92759 |
| E | General transcription factor iih subunit 2, P44 | protein | 366 | 29% helix, 18% strand | — |
| F | General transcription factor iih subunit 3, P34 | protein | 263 | 39% helix, 18% strand | Q13889 |
| G | General transcription factor iih subunit 5, P8 | protein | 66 | 47% helix, 12% strand | Q6ZYL4 |
| H | Cdk-activating kinase assembly factor MAT1 | protein | 210 | 64% helix, 4% strand | P51948 |
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 | 1096 | 0.86 | 0.88 | 128 | empty |
| 2 | 194 | 0.82 | 0.97 | 31 | empty |
| 3 | 704 | 0.81 | 0.85 | 78 | empty |
| 4 | 427 | 0.76 | 0.85 | 41 | empty |
| 5 | 734 | 0.71 | 0.78 | 70 | empty |
Interfaces
14 interfaces between chains.
- B–C · 3472 Ų buried · 36 hydrogen bonds · protein-protein
- C–F · 2654 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2516 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1796 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 1709 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NMI · Cryo-EM structure of the human TFIIH core complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q13889 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 3 (Q13889) · a predicted model of the same protein · chain F against A, TM-score 0.92
- P51948 · AlphaFold monomer V2.0 prediction for cdk-activating kinase assembly factor MAT1 (P51948) · a predicted model of the same protein · chain H against A, TM-score 0.75
- Q6ZYL4 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 5 (Q6ZYL4) · a predicted model of the same protein · chain G against A, TM-score 0.75
- Q92759 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 4 (Q92759) · a predicted model of the same protein · chain D against A, TM-score 0.74
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 Q92759
- Every structure of UniProt Q13889
- Every structure of UniProt Q6ZYL4
- Every structure of UniProt P51948
- Elsewhere: RCSB PDB 6NMI · PDBe 6NMI · UniProt Q92759 · UniProt Q13889 · UniProt Q6ZYL4 · UniProt P51948
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.