Research workbench
Crystal structure of RSFOLDER2 in its non-fluorescent off-state
Analyse Crystal structure of RSFOLDER2 in its non-fluorescent off-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AMF
- Type
- protein
- Length
- 927 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- PIA
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 230 | 10% helix, 51% strand | P42212 |
| B | Green fluorescent protein | protein | 229 | 10% helix, 51% strand | P42212 |
| C, D | Green fluorescent protein | protein | 234 | 15% helix, 50% strand | P42212 |
Ligands and binding sites
- PIA · [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.97 | 23 | PIA |
| 2 | 76 | 0.74 | 0.97 | 23 | PIA |
| 3 | 78 | 0.74 | 0.97 | 24 | PIA |
| 4 | 76 | 0.74 | 0.97 | 23 | PIA |
| 5 | 113 | 0.71 | 0.92 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–C · 588 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 385 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 284 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7AMF · Crystal structure of rsFolder2 in its non-fluorescent off-state · the same entry in another collection · chain D against D, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P42212
- Elsewhere: RCSB PDB 7AMF · PDBe 7AMF · UniProt P42212
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