Research workbench
GFP-binding darpin fusion GC_R11
Analyse GFP-binding darpin fusion GC_R11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MA3
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; R11
- UniProt
- P42212
- Ligands
- CRO
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Green fluorescent protein | protein | 227 | 11% helix, 52% strand | P42212 |
| A | R11 | protein | 302 | 51% helix, 0% strand | — |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains B
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.77 | 0.97 | 26 | CRO |
| 2 | 548 | 0.71 | 0.80 | 59 | empty |
| 3 | 486 | 0.68 | 0.79 | 59 | EDO |
| 4 | 243 | 0.62 | 0.81 | 39 | EDO |
| 5 | 121 | 0.49 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- B–A · 1595 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (chromophore).
Compared structures
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 5MA3 · PDBe 5MA3 · UniProt P42212
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