Research workbench
Phototoxic fluorescent protein killerorange
Analyse Phototoxic fluorescent protein killerorange in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZFS
- Type
- protein
- Length
- 1,147 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Killerorange
- Ligands
- 4M9
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Killerorange | protein | 233 | 6% helix, 51% strand | — |
| C, D, E | Killerorange | protein | 227 | 7% helix, 52% strand | — |
Ligands and binding sites
- 4M9 · (4Z)-4-imino-4-[(4Z)-4-(1H-indol-3-ylmethylidene)-5-oxo-1-(2-oxoethyl)-4,5-dihydro-1H-imidazol-2-yl]butanamide · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.85 | 117 | empty |
| 2 | 182 | 0.83 | 0.97 | 42 | 4M9 |
| 3 | 162 | 0.82 | 0.98 | 38 | 4M9 |
| 4 | 164 | 0.82 | 0.97 | 36 | 4M9 |
| 5 | 167 | 0.82 | 0.97 | 40 | 4M9 |
Interfaces
7 interfaces between chains.
- A–D · 1513 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 1491 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 713 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 289 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4ZFS · PDBe 4ZFS
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