MolNFT v1 · #122414 · protein
X-ray structure of the N-terminal domain of human doublecortin
5IOI · Neuronal migration protein doublecortin: “X-ray structure of the N-terminal domain of human doublecortin”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #122414 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IOI
- Type
- protein
- Length
- 582 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal migration protein doublecortin
- UniProt
- O43602
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Neuronal migration protein doublecortin | protein | 107 | 14% helix, 23% strand | O43602 |
| B | Neuronal migration protein doublecortin | protein | 88 | 17% helix, 26% strand | O43602 |
| C | Neuronal migration protein doublecortin | protein | 96 | 16% helix, 26% strand | O43602 |
| D | Neuronal migration protein doublecortin | protein | 89 | 17% helix, 26% strand | O43602 |
| F | Neuronal migration protein doublecortin | protein | 95 | 16% helix, 26% strand | O43602 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.72 | 0.81 | 67 | empty |
| 2 | 287 | 0.68 | 0.83 | 47 | empty |
| 3 | 260 | 0.50 | 0.74 | 29 | empty |
| 4 | 200 | 0.46 | 0.74 | 29 | empty |
| 5 | 115 | 0.38 | 0.75 | 23 | empty |
Interfaces
13 interfaces between chains.
- A–E · 1052 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 652 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 635 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 599 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 591 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5IOI · X-ray structure of the N-terminal domain of human doublecortin · the same entry in another collection · chain F against F, TM-score 1.00
- O43602 · AlphaFold monomer V2.0 prediction for neuronal migration protein doublecortin (O43602) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O43602
- Elsewhere: RCSB PDB 5IOI · PDBe 5IOI · UniProt O43602
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