MolNFT v1 · #116092 · protein + DNA
Transcription factor-DNA complex
5D39 · Signal transducer and activator of transcription 6: “Transcription factor-DNA complex”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #116092 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D39
- Type
- protein + DNA
- Length
- 2,028 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal transducer and activator of transcription 6; DNA (5'…
- UniProt
- P42226
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal transducer and activator of transcription 6 | protein | 489 | 43% helix, 18% strand | P42226 |
| B | Signal transducer and activator of transcription 6 | protein | 484 | 43% helix, 20% strand | P42226 |
| C | Signal transducer and activator of transcription 6 | protein | 484 | 44% helix, 21% strand | P42226 |
| D | Signal transducer and activator of transcription 6 | protein | 487 | 42% helix, 21% strand | P42226 |
| N, F | DNA (5'- D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)- 3') | dna | 21 | — | — |
| M, E | DNA (5'- D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)- 3') | dna | 21 | — | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.75 | 0.78 | 78 | empty |
| 2 | 517 | 0.69 | 0.79 | 39 | empty |
| 3 | 426 | 0.67 | 0.80 | 34 | empty |
| 4 | 386 | 0.67 | 0.80 | 34 | empty |
| 5 | 345 | 0.67 | 0.81 | 33 | empty |
Interfaces
13 interfaces between chains.
- B–D · 1303 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1295 Ų buried · 35 hydrogen bonds · protein-protein
- N–M · 906 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- E–F · 877 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–B · 594 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
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 P42226
- Elsewhere: RCSB PDB 5D39 · PDBe 5D39 · UniProt P42226
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