MolNFT v1 · #161315 · protein
Structure of the tripartite motif of KAP1/TRIM28
6QAJ · ENDOLYSIN,TRANSCRIPTION intermediary factor 1-beta: “Structure of the tripartite motif of KAP1/TRIM28”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.75). MolNFT v1 #161315 on GenesisL1: 3D structure, binding…
- PDB
- 6QAJ
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,TRANSCRIPTION intermediary factor 1-beta
- EC
- 3.2.1.17, 2.3.2.27
- UniProt
- P00720, Q13263
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,TRANSCRIPTION intermediary factor 1-beta (EC 3.2.1.17, 2.3.2.27) | protein | 439 | 55% helix, 9% strand | P00720, Q13263 |
| B | ENDOLYSIN,TRANSCRIPTION intermediary factor 1-beta (EC 3.2.1.17, 2.3.2.27) | protein | 441 | 55% helix, 8% strand | P00720, Q13263 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.75 | 0.79 | 79 | empty |
| 2 | 665 | 0.73 | 0.79 | 57 | empty |
| 3 | 58 | 0.66 | 0.94 | 19 | empty |
| 4 | 449 | 0.60 | 0.76 | 44 | empty |
| 5 | 56 | 0.59 | 0.91 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 7053 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6QAJ · Structure of the tripartite motif of KAP1/TRIM28 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13263 · AlphaFold monomer V2.0 prediction for transcription intermediary factor 1-beta (Q13263) · a predicted model of the same protein · chain A against A, TM-score 0.51
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 P00720
- Every structure of UniProt Q13263
- Elsewhere: RCSB PDB 6QAJ · PDBe 6QAJ · UniProt P00720 · UniProt Q13263
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