Research workbench
X-ray structure of branchiostoma floridae fluorescent protein LANFP10G
Analyse X-ray structure of branchiostoma floridae fluorescent protein LANFP10G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MAS
- Type
- protein
- Length
- 1,720 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- C3YRA2
- Ligands
- CR2
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Uncharacterized protein | protein | 215 | 10% helix, 57% strand | C3YRA2 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 7 copies · chains B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.87 | 0.89 | 112 | empty |
| 2 | 938 | 0.87 | 0.89 | 105 | empty |
| 3 | 123 | 0.79 | 0.98 | 34 | CR2 |
| 4 | 111 | 0.77 | 0.97 | 33 | CR2 |
| 5 | 96 | 0.77 | 0.98 | 32 | CR2 |
Interfaces
13 interfaces between chains.
- B–D · 1220 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1204 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1176 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 1174 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1007 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 6MAS · X-ray Structure of Branchiostoma floridae fluorescent protein lanFP10G · 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
- Every structure of UniProt C3YRA2
- Elsewhere: RCSB PDB 6MAS · PDBe 6MAS · UniProt C3YRA2
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