MolNFT v1 · #149942 · protein
The structure of twitch-2B N532F
6GEZ · Green fluorescent PROTEIN,OPTIMIZED ratiometric calcium…: “The structure of twitch-2B N532F”. X-ray diffraction, 3 ligands (CRF, CR2, CA), 11 pockets (best druggability 0.77). MolNFT v1 #149942 on GenesisL1: 3D structure, binding…
- PDB
- 6GEZ
- Type
- protein
- Length
- 1,063 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent PROTEIN,OPTIMIZED ratiometric calcium SENSOR,GREEN fluorescent…
- UniProt
- P42212, W5IDB2
- Ligands
- CRF, CR2, CA
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent PROTEIN,OPTIMIZED ratiometric calcium SENSOR,GREEN fluorescent PROTEIN,GREEN fluorescent protein | protein | 531 | 18% helix, 45% strand | P42212, W5IDB2 |
| B | Green fluorescent PROTEIN,OPTIMIZED ratiometric calcium SENSOR,GREEN fluorescent PROTEIN,GREEN fluorescent protein | protein | 532 | 18% helix, 45% strand | P42212, W5IDB2 |
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 · 2 copies · chains A, B
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.77 | 0.99 | 23 | CRF |
| 2 | 1003 | 0.77 | 0.79 | 76 | empty |
| 3 | 682 | 0.76 | 0.82 | 62 | FMT |
| 4 | 986 | 0.75 | 0.78 | 78 | empty |
| 5 | 73 | 0.74 | 0.98 | 23 | CRF |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 covalent (chromophore, covalent ligand).
Compared structures
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 W5IDB2
- Elsewhere: RCSB PDB 6GEZ · PDBe 6GEZ · UniProt P42212 · UniProt W5IDB2
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