MolNFT v1 · #112068 · protein
Tctp contains a BH3-like domain, which instead of inhibiting, activates BCL-xl
4Z9V · BCL-2-like protein 1,APOPTOSIS regulator BCL-xl: “Tctp contains a BH3-like domain, which instead of inhibiting, activates BCL-xl”. X-ray diffraction, 2 ligands (BCT, NA), 3 pockets (best druggability 0.72). MolNFT v1 #112068 on…
- PDB
- 4Z9V
- Type
- protein
- Length
- 418 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1,APOPTOSIS regulator BCL-xl; Translationally-controlled tumor protein
- UniProt
- Q07817, P13693
- Ligands
- BCT, NA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1,APOPTOSIS regulator BCL-xl | protein | 153 | 72% helix, 1% strand | Q07817 |
| B | BCL-2-like protein 1,APOPTOSIS regulator BCL-xl | protein | 151 | 75% helix, 1% strand | Q07817 |
| C | Translationally-controlled tumor protein | protein | 15 | 73% helix, 0% strand | P13693 |
| D | Translationally-controlled tumor protein | protein | 16 | 69% helix, 0% strand | P13693 |
| E, G, H | Translationally-controlled tumor protein | protein | 21 | 38% helix, 10% strand | P13693 |
| F | Translationally-controlled tumor protein | protein | 20 | 40% helix, 10% strand | P13693 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B, H, G
- NA · Sodium ion · metal · 2 copies · chains B, F, A, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.72 | 0.79 | 72 | BCT, NA |
| 2 | 110 | 0.49 | 0.80 | 22 | empty |
| 3 | 65 | 0.31 | 0.74 | 12 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2123 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 950 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 846 Ų buried · 13 hydrogen bonds · protein-protein
- B–G · 815 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 810 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4Z9V · TCTP contains a BH3-like domain, which instead of inhibiting, activates Bcl-xL · the same entry in another collection · chain H against H, TM-score 1.00
- Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain B against A, TM-score 0.77
- P13693 · AlphaFold monomer V2.0 prediction for translationally-controlled tumor protein (P13693) · a predicted model of the same protein · chain C against A, TM-score 0.65
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 Q07817
- Every structure of UniProt P13693
- Elsewhere: RCSB PDB 4Z9V · PDBe 4Z9V · UniProt Q07817 · UniProt P13693
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