MolNFT v1 · #159064 · protein + DNA
Human TCF4 C-terminal bhlh domain in complex with 13-bp oligonucleotide containing E-box sequence
6OD3 · Transcription factor 4: “Human TCF4 C-terminal bhlh domain in complex with 13-bp oligonucleotide containing E-box sequence”. X-ray diffraction, 1 ligand (CL), 13 pockets (best druggability 0.79). MolNFT v1 #159064 on GenesisL1: 3D…
- PDB
- 6OD3
- Type
- protein + DNA
- Length
- 523 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor 4; DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
- UniProt
- P15884
- Ligands
- CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Transcription factor 4 | protein | 62 | 82% helix, 0% strand | P15884 |
| B | Transcription factor 4 | protein | 61 | 82% helix, 0% strand | P15884 |
| X, Y, Z | DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3') | dna | 13 | — | — |
| W | DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3') | dna | 12 | — | — |
| F | Transcription factor 4 | protein | 60 | 83% helix, 0% strand | P15884 |
| G | Transcription factor 4 | protein | 55 | 76% helix, 4% strand | P15884 |
| H | Transcription factor 4 | protein | 61 | 61% helix, 0% strand | P15884 |
| I | Transcription factor 4 | protein | 59 | 80% helix, 0% strand | P15884 |
| J | Transcription factor 4 | protein | 52 | 71% helix, 0% strand | P15884 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, X, B, W, H, Y, Z
- PG4 · Tetraethylene glycol · additive · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.79 | 0.98 | 22 | CL |
| 2 | 837 | 0.79 | 0.82 | 70 | empty |
| 3 | 102 | 0.79 | 0.99 | 22 | CL |
| 4 | 418 | 0.60 | 0.76 | 45 | EDO |
| 5 | 158 | 0.57 | 0.82 | 30 | empty |
Interfaces
28 interfaces between chains.
- G–H · 1158 Ų buried · 2 hydrogen bonds · protein-protein
- I–J · 1119 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 1009 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1002 Ų buried · 2 hydrogen bonds · protein-protein
- Y–Z · 542 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 6OD3 · Human TCF4 C-terminal bHLH domain in Complex with 13-bp Oligonucleotide Containing E-box… · the same entry in another collection · chain J against J, TM-score 1.00
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 6OD3 · PDBe 6OD3 · UniProt P15884
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