Research workbench
Crystal structure of tagbfp fluorescent protein
Analyse Crystal structure of tagbfp fluorescent protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M24
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tagbfp
- Ligands
- NRP, CL
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tagbfp | protein | 225 | 4% helix, 56% strand | — |
| B | Tagbfp | protein | 227 | 7% helix, 55% strand | — |
| C | Tagbfp | protein | 226 | 8% helix, 56% strand | — |
| D | Tagbfp | protein | 224 | 5% helix, 56% strand | — |
Ligands and binding sites
- NRP · {4-[(4-hydroxyphenyl)methylidene]-2-[(1E)-3-methylbutanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, D, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.84 | 0.85 | 89 | empty |
| 2 | 86 | 0.77 | 0.99 | 25 | NRP |
| 3 | 85 | 0.77 | 0.99 | 25 | NRP |
| 4 | 89 | 0.76 | 0.98 | 24 | NRP |
| 5 | 82 | 0.76 | 0.98 | 24 | NRP |
Interfaces
6 interfaces between chains.
- C–D · 1464 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 993 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 991 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand, additive adduct).
Compared structures
- 3M24 · Crystal structure of TagBFP 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 3M24 · PDBe 3M24
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.