MolNFT v1 · #159066 · protein + DNA
Human TCF4 C-terminal bhlh domain in complex with 12-bp oligonucleotide containing E-box sequence with 5-carboxylcytosines
6OD5 · Transcription factor 4: “Human TCF4 C-terminal bhlh domain in complex with 12-bp oligonucleotide containing E-box sequence with…”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.83). MolNFT v1 #159066 on GenesisL1…
- PDB
- 6OD5
- Type
- protein + DNA
- Length
- 289 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor 4; DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
- UniProt
- P15884
- Ligands
- CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transcription factor 4 | protein | 62 | 84% helix, 0% strand | P15884 |
| B | Transcription factor 4 | protein | 60 | 77% helix, 0% strand | P15884 |
| X, Y | DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3') | dna | 12 | — | — |
| C | Transcription factor 4 | protein | 59 | 78% helix, 0% strand | P15884 |
| E | DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, Y, C, E, F
- GOL · Glycerol · additive · chains X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.83 | 0.99 | 23 | empty |
| 2 | 144 | 0.82 | 0.99 | 23 | empty |
| 3 | 58 | 0.36 | 0.79 | 13 | empty |
| 4 | 90 | 0.35 | 0.76 | 25 | empty |
| 5 | 68 | 0.35 | 0.77 | 14 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1041 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1032 Ų buried · 4 hydrogen bonds · protein-protein
- X–Y · 558 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- E–F · 524 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- D–E · 508 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 6OD5 · Human TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucleotide Containing E-box… · the same entry in another collection · chain F against F, TM-score 1.00
- P15884 · AlphaFold monomer V2.0 prediction for transcription factor 4 (P15884) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P15884
- Elsewhere: RCSB PDB 6OD5 · PDBe 6OD5 · UniProt P15884
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