MolNFT v1 · #13017 · protein
Crystal structure of a cu-bound green fluorescent protein zn biosensor
1KYR: “Crystal structure of a cu-bound green fluorescent protein zn biosensor”. X-ray diffraction, 3 ligands (CRG, CU, MG), 2 pockets (best druggability 0.76). MolNFT v1 #13017 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KYR
- Type
- protein
- Length
- 224 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRG, CU, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 224 | 12% helix, 53% strand | P42212 |
Ligands and binding sites
- CRG · [2-(1-amino-2-hydroxy-propyl)-4-(3H-imidazol-4-ylmethylene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · chains A
- CU · Copper (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.76 | 0.95 | 28 | CRG, CU |
| 2 | 84 | 0.34 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1KYR · Crystal Structure of a Cu-bound Green Fluorescent Protein Zn Biosensor · 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 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 P42212
- Elsewhere: RCSB PDB 1KYR · PDBe 1KYR · UniProt P42212
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