Research workbench
Crystal structure of eyfp HIS148SER
Analyse Crystal structure of eyfp HIS148SER in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VIO
- Type
- protein
- Length
- 1,801 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein GFP
- UniProt
- A0A5J6CYR6
- Ligands
- CR2
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, H | Green fluorescent protein GFP | protein | 226 | 9% helix, 52% strand | A0A5J6CYR6 |
| B, D | Green fluorescent protein GFP | protein | 225 | 10% helix, 52% strand | A0A5J6CYR6 |
| C | Green fluorescent protein GFP | protein | 224 | 10% helix, 53% strand | A0A5J6CYR6 |
| G | Green fluorescent protein GFP | protein | 223 | 10% helix, 53% strand | A0A5J6CYR6 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.80 | 0.81 | 121 | empty |
| 2 | 972 | 0.77 | 0.80 | 78 | empty |
| 3 | 97 | 0.77 | 0.97 | 26 | CR2 |
| 4 | 100 | 0.77 | 0.97 | 23 | CR2 |
| 5 | 98 | 0.77 | 0.97 | 25 | CR2 |
Interfaces
15 interfaces between chains.
- B–H · 594 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 589 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 529 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 516 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 515 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 6VIO · Crystal structure of eYFP His148Ser · the same entry in another collection · chain H against H, 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 A0A5J6CYR6
- Elsewhere: RCSB PDB 6VIO · PDBe 6VIO · UniProt A0A5J6CYR6
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