Research workbench
Crystal structure of the photoconverted green fluorescent protein NOWGFP_CONV (the variant of cyan cerulean) at pH 7.0
Analyse Crystal structure of the photoconverted green fluorescent protein NOWGFP_CONV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RYW
- Type
- protein
- Length
- 681 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NOWGFP_CONV
- Ligands
- CRF
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NOWGFP_CONV | protein | 227 | 11% helix, 52% strand | — |
Ligands and binding sites
- CRF · [(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.79 | 0.98 | 23 | CRF |
| 2 | 140 | 0.79 | 0.96 | 24 | CRF |
| 3 | 103 | 0.75 | 0.96 | 23 | CRF |
| 4 | 590 | 0.69 | 0.78 | 80 | empty |
| 5 | 223 | 0.54 | 0.78 | 32 | empty |
Interfaces
2 interfaces between chains.
- B–C · 650 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4RYW · Crystal structure of the photoconverted green fluorescent protein NowGFP_conv (the… · 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
- Elsewhere: RCSB PDB 4RYW · PDBe 4RYW
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