MolNFT v1 · #122436 · protein
X-ray structure of the C-terminal domain of human doublecortin
5IP4 · XA4551 nanobody against C-dcx: “X-ray structure of the C-terminal domain of human doublecortin”. X-ray diffraction, 2 pockets (best druggability 0.48). MolNFT v1 #122436 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IP4
- Type
- protein
- Length
- 383 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- XA4551 nanobody against C-dcx; Neuronal migration protein doublecortin
- UniProt
- O43602
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | XA4551 nanobody against C-dcx | protein | 109 | 6% helix, 51% strand | — |
| B | XA4551 nanobody against C-dcx | protein | 110 | 5% helix, 53% strand | — |
| D | Neuronal migration protein doublecortin | protein | 80 | 19% helix, 30% strand | O43602 |
| E | Neuronal migration protein doublecortin | protein | 84 | 21% helix, 27% strand | O43602 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.48 | 0.86 | 18 | empty |
| 2 | 76 | 0.48 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 723 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 685 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 62 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5IP4 · X-ray structure of the C-terminal domain of human doublecortin · the same entry in another collection · chain B against B, TM-score 1.00
- O43602 · AlphaFold monomer V2.0 prediction for neuronal migration protein doublecortin (O43602) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 5IP4 · PDBe 5IP4 · UniProt O43602
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