Research workbench
Crystal structure of a distal-less homeobox protein 5 (DLX5) from homo sapiens at 1.85 a resolution
Analyse Crystal structure of a distal-less homeobox protein 5 (DLX5) from homo sapiens… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDU
- Type
- protein + DNA
- Length
- 178 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein dlx-5; (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
- UniProt
- P56178
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein dlx-5 | protein | 61 | 70% helix, 0% strand | P56178 |
| B, C, E | (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG) | dna | 14 | — | — |
| D | Homeobox protein dlx-5 | protein | 62 | 71% helix, 0% strand | P56178 |
| F | (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG) | dna | 13 | — | — |
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 | 535 | 0.72 | 0.81 | 66 | empty |
| 2 | 186 | 0.54 | 0.79 | 25 | empty |
| 3 | 54 | 0.43 | 0.83 | 15 | empty |
| 4 | 110 | 0.41 | 0.77 | 26 | empty |
Interfaces
11 interfaces between chains.
- A–B · 580 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 569 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- E–F · 561 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–C · 553 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–F · 524 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 4RDU · Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A… · the same entry in another collection · chain F against F, TM-score 1.00
- P56178 · AlphaFold monomer V2.0 prediction for homeobox protein dlx-5 (P56178) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P56178
- Elsewhere: RCSB PDB 4RDU · PDBe 4RDU · UniProt P56178
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