Research workbench
Structure of plexin D1 intracellular domain
Analyse Structure of plexin D1 intracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6R
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-D1
- UniProt
- Q3UH93
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-D1 | protein | 505 | 58% helix, 8% strand | Q3UH93 |
| B | Plexin-D1 | protein | 503 | 59% helix, 9% strand | Q3UH93 |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.71 | 0.75 | 89 | empty |
| 2 | 529 | 0.69 | 0.79 | 59 | empty |
| 3 | 187 | 0.62 | 0.83 | 30 | empty |
| 4 | 277 | 0.60 | 0.79 | 31 | empty |
| 5 | 243 | 0.60 | 0.80 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 453 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 Q3UH93
- Elsewhere: RCSB PDB 5V6R · PDBe 5V6R · UniProt Q3UH93
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