Research workbench
Crystal structure of photoinhibitable INTERSECTIN1 containing wildtype LOV2 domain in complex with CDC42
Analyse Crystal structure of photoinhibitable INTERSECTIN1 containing wildtype LOV2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HZK
- Type
- protein
- Length
- 1,283 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 42 homolog; Intersectin-1,NPH1-1,INTERSECTIN-1
- UniProt
- P60953, Q15811, O49003
- Ligands
- GDP, FMN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division control protein 42 homolog | protein | 176 | 35% helix, 22% strand | P60953 |
| B | Intersectin-1,NPH1-1,INTERSECTIN-1 | protein | 460 | 53% helix, 18% strand | Q15811, O49003 |
| D | Intersectin-1,NPH1-1,INTERSECTIN-1 | protein | 471 | 51% helix, 18% strand | Q15811, O49003 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.82 | 0.83 | 98 | FMN |
| 2 | 623 | 0.79 | 0.84 | 71 | empty |
| 3 | 391 | 0.72 | 0.83 | 44 | FMN |
| 4 | 494 | 0.67 | 0.78 | 50 | GDP |
| 5 | 519 | 0.66 | 0.77 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1406 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1387 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 885 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 869 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5HZK · Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in… · the same entry in another collection · chain D against D, TM-score 1.00
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q15811 · AlphaFold monomer V2.0 prediction for intersectin-1 (Q15811) · a predicted model of the same protein · chain D against A, TM-score 0.68
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 P60953
- Every structure of UniProt Q15811
- Every structure of UniProt O49003
- Elsewhere: RCSB PDB 5HZK · PDBe 5HZK · UniProt P60953 · UniProt Q15811 · UniProt O49003
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