MolNFT v1 · #165413 · protein
Helicase domain complex
6TUN · General transcription and DNA repair factor iih helicase…: “Helicase domain complex”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.61). MolNFT v1 #165413 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6TUN
- Type
- protein
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General transcription and DNA repair factor iih helicase subunit xpd; Cdk-activating…
- EC
- 3.6.4.12
- UniProt
- P18074, P51948
- Ligands
- CL
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12) | protein | 173 | 58% helix, 11% strand | P18074 |
| B | General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12) | protein | 170 | 58% helix, 11% strand | P18074 |
| D | Cdk-activating kinase assembly factor MAT1 | protein | 65 | 77% helix, 0% strand | P51948 |
| C | Cdk-activating kinase assembly factor MAT1 | protein | 65 | 77% helix, 0% strand | P51948 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.61 | 0.82 | 26 | empty |
| 2 | 170 | 0.56 | 0.81 | 26 | empty |
| 3 | 115 | 0.54 | 0.83 | 20 | empty |
| 4 | 137 | 0.52 | 0.81 | 24 | empty |
| 5 | 112 | 0.40 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1969 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 801 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TUN · Helicase domain complex · the same entry in another collection · chain C against C, TM-score 1.00
- P51948 · AlphaFold monomer V2.0 prediction for cdk-activating kinase assembly factor MAT1 (P51948) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P18074 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P51948
- Elsewhere: RCSB PDB 6TUN · PDBe 6TUN · UniProt P18074 · UniProt P51948
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.