Research workbench
The plexin D1 intracellular region in complex with GIPC1
Analyse The plexin D1 intracellular region in complex with GIPC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6T
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-D1; PDZ domain-containing protein GIPC1
- UniProt
- Q3UH93, Q9Z0G0
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-D1 | protein | 516 | 57% helix, 9% strand | Q3UH93 |
| B | PDZ domain-containing protein GIPC1 | protein | 161 | 15% helix, 29% strand | Q9Z0G0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.66 | 0.87 | 27 | empty |
| 2 | 328 | 0.64 | 0.79 | 34 | empty |
| 3 | 327 | 0.61 | 0.78 | 31 | empty |
| 4 | 229 | 0.57 | 0.79 | 26 | empty |
| 5 | 174 | 0.47 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5V6T · The Plexin D1 intracellular region in complex with GIPC1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q3UH93 · AlphaFold monomer V2.0 prediction for plexin-D1 (Q3UH93) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9Z0G0 · AlphaFold monomer V2.0 prediction for PDZ domain-containing protein GIPC1 (Q9Z0G0) · a predicted model of the same protein · chain B against A, TM-score 0.59
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
- Every structure of UniProt Q9Z0G0
- Elsewhere: RCSB PDB 5V6T · PDBe 5V6T · UniProt Q3UH93 · UniProt Q9Z0G0
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