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Structure of the GFP:GFP-nanobody complex at 2.8 a resolution in spacegroup P21212
Analyse Structure of the GFP:GFP-nanobody complex at 2.8 a resolution in spacegroup… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OGO
- Type
- protein
- Length
- 1,369 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; GFP-nanobody
- UniProt
- P42212
- Ligands
- CRO
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 231 | 12% helix, 50% strand | P42212 |
| B | Green fluorescent protein | protein | 224 | 13% helix, 52% strand | P42212 |
| C | Green fluorescent protein | protein | 227 | 11% helix, 51% strand | P42212 |
| D | Green fluorescent protein | protein | 225 | 11% helix, 52% strand | P42212 |
| E, F | GFP-nanobody | protein | 115 | 3% helix, 50% strand | — |
| G | GFP-nanobody | protein | 116 | 5% helix, 51% strand | — |
| H | GFP-nanobody | protein | 116 | 3% helix, 51% 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 · 4 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, E, D, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.79 | 0.98 | 27 | CRO |
| 2 | 101 | 0.79 | 0.99 | 31 | CRO |
| 3 | 96 | 0.77 | 0.98 | 27 | CRO |
| 4 | 101 | 0.76 | 0.97 | 27 | CRO |
| 5 | 679 | 0.71 | 0.78 | 83 | IPA |
Interfaces
14 interfaces between chains.
- C–F · 718 Ų buried · 18 hydrogen bonds · protein-protein
- B–G · 714 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 690 Ų buried · 11 hydrogen bonds · protein-protein
- C–H · 382 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 377 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3OGO · Structure of the GFP:GFP-nanobody complex at 2.8 A resolution in spacegroup P21212 · the same entry in another collection · chain H against H, 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 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 P42212
- Elsewhere: RCSB PDB 3OGO · PDBe 3OGO · UniProt P42212
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