Research workbench
Structure of CDX1 bound to hydroxymethylated DNA
Analyse Structure of CDX1 bound to hydroxymethylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q3O
- Type
- protein + DNA
- Length
- 389 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.78
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- hydroxymethylated DNA (18-MER); Homeobox protein CDX-1
- UniProt
- P47902
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.78 · 5 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | hydroxymethylated DNA (18-MER) | dna | 18 | — | — |
| H, I, J, L | hydroxymethylated DNA (18-MER) | dna | 18 | — | — |
| K, G | Homeobox protein CDX-1 | protein | 61 | 62% helix, 0% strand | P47902 |
| C | Homeobox protein CDX-1 | protein | 63 | 63% helix, 0% strand | P47902 |
| E | Homeobox protein CDX-1 | protein | 60 | 65% helix, 0% strand | P47902 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.73 | 0.83 | 33 | empty |
| 2 | 497 | 0.73 | 0.82 | 45 | empty |
| 3 | 623 | 0.72 | 0.80 | 68 | empty |
| 4 | 286 | 0.63 | 0.81 | 30 | empty |
| 5 | 341 | 0.63 | 0.79 | 32 | empty |
Interfaces
31 interfaces between chains.
- B–I · 760 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- D–J · 751 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–H · 749 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- F–L · 741 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- I–C · 625 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- P47902 · AlphaFold monomer V2.0 prediction for homeobox protein cdx-1 (P47902) · a predicted model of the same protein · chain E against A, TM-score 0.91
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 P47902
- Elsewhere: RCSB PDB 7Q3O · PDBe 7Q3O · UniProt P47902
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