Research workbench
Crystal structure of amphioxus GFPC1A
Analyse Crystal structure of amphioxus GFPC1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DKM
- Type
- protein
- Length
- 1,704 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amphioxus green fluorescent protein, GFPC1A
- UniProt
- C3YRA3
- Ligands
- CR2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Amphioxus green fluorescent protein, GFPC1A | protein | 213 | 9% helix, 57% strand | C3YRA3 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.85 | 0.87 | 143 | empty |
| 2 | 84 | 0.76 | 0.98 | 27 | CR2 |
| 3 | 81 | 0.76 | 0.98 | 26 | CR2 |
| 4 | 82 | 0.75 | 0.98 | 25 | CR2 |
| 5 | 82 | 0.75 | 0.98 | 27 | CR2 |
Interfaces
15 interfaces between chains.
- D–H · 1091 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 1068 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 1057 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1050 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 791 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 4DKM · Crystal Structure of Amphioxus GFPc1a · 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 C3YRA3
- Elsewhere: RCSB PDB 4DKM · PDBe 4DKM · UniProt C3YRA3
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