MolNFT v1 · #71033 · protein
Crystal structure of tagrfp fluorescent protein
3M22: “Crystal structure of tagrfp fluorescent protein”. X-ray diffraction, 1 ligand (NRQ), 14 pockets (best druggability 0.77). MolNFT v1 #71033 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3M22
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tagrfp
- Ligands
- NRQ
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tagrfp | protein | 223 | 6% helix, 57% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.99 | 24 | NRQ |
| 2 | 77 | 0.75 | 0.98 | 26 | NRQ |
| 3 | 70 | 0.73 | 0.98 | 22 | NRQ |
| 4 | 62 | 0.71 | 0.98 | 21 | NRQ |
| 5 | 581 | 0.69 | 0.78 | 45 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1560 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1544 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 123 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 3M22 · Crystal structure of TagRFP fluorescent protein · 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 3M22 · PDBe 3M22
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