MolNFT v1 · #122908 · protein
C-terminal domain of ECOR124I hsdr subunit fused with the pH-sensitive GFP variant ratiometric phluorin
5J3N · Green fluorescent PROTEIN,HSDR: “C-terminal domain of ECOR124I hsdr subunit fused with the pH-sensitive GFP variant ratiometric phluorin”. X-ray diffraction, 1 ligand (GYS), 9 pockets (best druggability 0.76). MolNFT v1 #122908 on…
- PDB
- 5J3N
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent PROTEIN,HSDR
- UniProt
- P42212, Q304R3
- Ligands
- GYS
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent PROTEIN,HSDR | protein | 385 | 31% helix, 31% strand | P42212, Q304R3 |
| B | Green fluorescent PROTEIN,HSDR | protein | 229 | 10% helix, 52% strand | P42212, Q304R3 |
Ligands and binding sites
- GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.76 | 0.98 | 24 | GYS |
| 2 | 68 | 0.74 | 0.98 | 20 | GYS |
| 3 | 601 | 0.66 | 0.76 | 48 | empty |
| 4 | 139 | 0.58 | 0.83 | 26 | empty |
| 5 | 156 | 0.50 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1433 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 5J3N · C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant… · the same entry in another collection · chain A against A, 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 0.99
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
- Every structure of UniProt Q304R3
- Elsewhere: RCSB PDB 5J3N · PDBe 5J3N · UniProt P42212 · UniProt Q304R3
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