Research workbench
X-ray structure of branchiostoma floridae fluorescent protein LANFP10A
Analyse X-ray structure of branchiostoma floridae fluorescent protein LANFP10A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M9X
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein LANFP10A
- UniProt
- C3YRA2
- Ligands
- JBY
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fluorescent protein LANFP10A | protein | 215 | 10% helix, 56% strand | C3YRA2 |
Ligands and binding sites
- JBY · (2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl) methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic 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
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.87 | 0.89 | 101 | empty |
| 2 | 97 | 0.77 | 0.97 | 31 | JBY |
| 3 | 96 | 0.76 | 0.97 | 27 | JBY |
| 4 | 84 | 0.75 | 0.98 | 29 | JBY |
| 5 | 71 | 0.73 | 0.97 | 20 | JBY |
Interfaces
6 interfaces between chains.
- C–D · 1216 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1204 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1003 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 998 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6M9X · X-ray Structure of Branchiostoma floridae fluorescent protein lanFP10A · 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 6M9X · PDBe 6M9X · UniProt C3YRA2
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