Research workbench
Homeobox transcription factor CDX1 bound to methylated DNA
Analyse Homeobox transcription factor CDX1 bound to methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LUX
- Type
- protein + DNA
- Length
- 195 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*CP*CP*TP*C)-3'); Homeobox protein…
- UniProt
- P47902
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*CP*CP*TP*C)-3') | dna | 17 | — | — |
| K | Homeobox protein cdx-1 | protein | 63 | 70% helix, 0% strand | P47902 |
| B | DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*CP*CP*TP*CP*C)-3') | dna | 18 | — | — |
| L | Homeobox protein cdx-1 | protein | 62 | 69% helix, 0% strand | P47902 |
| F | DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM) P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') | dna | 17 | — | — |
| E | DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM) P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') | dna | 18 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.73 | 0.80 | 51 | empty |
| 2 | 692 | 0.72 | 0.79 | 60 | empty |
| 3 | 82 | 0.36 | 0.76 | 12 | empty |
| 4 | 61 | 0.35 | 0.79 | 11 | empty |
Interfaces
11 interfaces between chains.
- B–E · 786 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–F · 734 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–K · 582 Ų buried · 19 hydrogen bonds · protein-nucleic
- K–F · 571 Ų buried · 11 hydrogen bonds · protein-nucleic
- L–E · 566 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
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 P47902
- Elsewhere: RCSB PDB 5LUX · PDBe 5LUX · UniProt P47902
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