Research workbench
GFP-binding darpin fusion GC_K11
Analyse GFP-binding darpin fusion GC_K11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MA5
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; K11
- UniProt
- P42212
- Ligands
- CRO, NA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Green fluorescent protein | protein | 227 | 11% helix, 51% strand | P42212 |
| A | K11 | protein | 298 | 51% helix, 0% strand | — |
| D | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
| C | K11 | protein | 288 | 52% 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 · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains A, C
- CIT · Citric acid · additive · 4 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A, D, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.78 | 0.98 | 24 | CRO |
| 2 | 106 | 0.78 | 0.97 | 24 | CRO |
| 3 | 379 | 0.73 | 0.83 | 39 | IPA |
| 4 | 439 | 0.70 | 0.81 | 46 | EDO |
| 5 | 401 | 0.68 | 0.81 | 52 | empty |
Interfaces
2 interfaces between chains.
- B–A · 1863 Ų buried · 20 hydrogen bonds · protein-protein
- D–C · 1772 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 5MA5 · PDBe 5MA5 · UniProt P42212
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