MolNFT v1 · #177023 · protein
Crystal structure of sfgfp complexed with the nanobody NB2 at 2.2 angstron resolution
7E53 · Green fluorescent protein: “Crystal structure of sfgfp complexed with the nanobody NB2 at 2.2 angstron resolution”. X-ray diffraction, 1 ligand (CRO), 1 pocket (best druggability 0.76). MolNFT v1 #177023 on GenesisL1: 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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