Research workbench
Crystal structure of the E2F5-DP1-P107 ternary complex
Analyse Crystal structure of the E2F5-DP1-P107 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TUV
- Type
- protein
- Length
- 462 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor DP1; Transcription factor E2F5; Retinoblastoma-like protein 1
- UniProt
- Q14186, Q15329, P28749
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor DP1 | protein | 107 | 49% helix, 21% strand | Q14186 |
| B | Transcription factor E2F5 | protein | 104 | 46% helix, 26% strand | Q15329 |
| C | Retinoblastoma-like protein 1 | protein | 29 | 45% helix, 17% strand | P28749 |
| D | Transcription factor DP1 | protein | 95 | 43% helix, 25% strand | Q14186 |
| E | Transcription factor E2F5 | protein | 103 | 41% helix, 27% strand | Q15329 |
| F | Retinoblastoma-like protein 1 | protein | 24 | 46% helix, 17% strand | P28749 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.80 | 0.98 | 18 | empty |
| 2 | 237 | 0.60 | 0.80 | 33 | empty |
| 3 | 266 | 0.59 | 0.79 | 38 | empty |
| 4 | 129 | 0.40 | 0.75 | 20 | empty |
| 5 | 99 | 0.35 | 0.74 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3056 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2580 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 726 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 516 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 493 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TUV · Crystal structure of the E2F5-DP1-p107 ternary complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q14186 · AlphaFold monomer V2.0 prediction for transcription factor dp-1 (Q14186) · a predicted model of the same protein · chain D against A, TM-score 0.82
- Q15329 · AlphaFold monomer V2.0 prediction for transcription factor E2F5 (Q15329) · a predicted model of the same protein · chain B against A, TM-score 0.73
- P28749 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 1 (P28749) · a predicted model of the same protein · chain C against A, TM-score 0.70
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 Q14186
- Every structure of UniProt Q15329
- Every structure of UniProt P28749
- Elsewhere: RCSB PDB 5TUV · PDBe 5TUV · UniProt Q14186 · UniProt Q15329 · UniProt P28749
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