Research workbench
Crystal structure of sfgfp complexed with the nanobody NB2 at 2.2 angstron resolution
Analyse Crystal structure of sfgfp complexed with the nanobody NB2 at 2.2 angstron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E53
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; Green fluorescent PROTEIN'S nanobody NB2
- UniProt
- A0A059PIQ0
- Ligands
- CRO
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 226 | 12% helix, 52% strand | A0A059PIQ0 |
| B | Green fluorescent PROTEIN'S nanobody NB2 | protein | 126 | 5% helix, 46% 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 A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.76 | 0.96 | 26 | CRO |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (chromophore, disulfide).
Compared structures
- 7E53 · Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution · the same entry in another collection · chain A 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 A0A059PIQ0
- Elsewhere: RCSB PDB 7E53 · PDBe 7E53 · UniProt A0A059PIQ0
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