Research workbench
Crystal structure of a domain-swapped dark-state sfgfp containing the unnatural amino acid ortho-nitrobenzyl-tyrosine (onby) at residue 66
Analyse Crystal structure of a domain-swapped dark-state sfgfp containing the unnatural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H01
- Type
- protein
- Length
- 921 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- A0A059PIQ0
- Ligands
- FHE
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 231 | 10% helix, 51% strand | A0A059PIQ0 |
| B, C, D | Green fluorescent protein | protein | 230 | 11% helix, 51% strand | A0A059PIQ0 |
Ligands and binding sites
- FHE · 2-[(4~{Z})-2-[(1~{R})-1-azanyl-2-oxidanylidene-propyl]-4-[[4-[(2-nitrophenyl)methoxy]phenyl]methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.82 | 0.97 | 42 | FHE |
| 2 | 171 | 0.81 | 0.96 | 40 | FHE |
| 3 | 171 | 0.80 | 0.95 | 37 | FHE |
| 4 | 291 | 0.79 | 0.90 | 54 | FHE |
| 5 | 1186 | 0.71 | 0.75 | 93 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5523 Ų buried · 101 hydrogen bonds · protein-protein
- B–D · 5499 Ų buried · 103 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 242 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 228 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 6H01 · Crystal structure of a domain-swapped dark-state sfGFP containing the unnatural amino… · 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 6H01 · PDBe 6H01 · UniProt A0A059PIQ0
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