MolNFT v1 · #113800 · protein
Darpin-based crystallization chaperones exploit molecular geometry as a screening dimension in protein crystallography
5AQB · 3G61_DB15V4: “Darpin-based crystallization chaperones exploit molecular geometry as a screening dimension in protein…”. X-ray diffraction, 1 ligand (CRO), 5 pockets (best druggability 0.78). MolNFT v1 #113800 on GenesisL1: 3D…
- PDB
- 5AQB
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3G61_DB15V4; Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3G61_DB15V4 | protein | 408 | 46% helix, 12% strand | — |
| B | Green fluorescent protein | protein | 228 | 12% helix, 51% strand | P42212 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.78 | 0.98 | 26 | CRO |
| 2 | 403 | 0.65 | 0.78 | 49 | empty |
| 3 | 63 | 0.41 | 0.81 | 16 | empty |
| 4 | 129 | 0.41 | 0.75 | 27 | empty |
| 5 | 73 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (chromophore, disulfide).
Compared structures
- 5AQB · DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening… · 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 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 5AQB · PDBe 5AQB · UniProt P42212
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