Research workbench
Mcardinal V218E
Analyse Mcardinal V218E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OJ0
- Type
- protein
- Length
- 896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein FP480
- UniProt
- D0VX33
- Ligands
- NRQ
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fluorescent protein FP480 | protein | 224 | 6% helix, 56% strand | D0VX33 |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.77 | 0.79 | 121 | empty |
| 2 | 95 | 0.77 | 0.98 | 26 | NRQ |
| 3 | 93 | 0.76 | 0.98 | 26 | NRQ |
| 4 | 94 | 0.76 | 0.98 | 28 | NRQ |
| 5 | 99 | 0.76 | 0.97 | 27 | NRQ |
Interfaces
6 interfaces between chains.
- A–D · 1595 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 385 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 248 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 87 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4OJ0 · mCardinal V218E · the same entry in another collection · chain A against A, TM-score 1.00
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 D0VX33
- Elsewhere: RCSB PDB 4OJ0 · PDBe 4OJ0 · UniProt D0VX33
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