Research workbench
Crystal structure of an ancestral GFP-like protein
Analyse Crystal structure of an ancestral GFP-like protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DXM
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- Ligands
- CR8, SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Green fluorescent protein | protein | 219 | 4% helix, 57% strand | — |
| B | Green fluorescent protein | protein | 220 | 5% helix, 56% strand | — |
| D | Green fluorescent protein | protein | 220 | 4% helix, 56% strand | — |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 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 | 1098 | 0.84 | 0.85 | 114 | empty |
| 2 | 85 | 0.76 | 0.98 | 29 | CR8 |
| 3 | 78 | 0.76 | 0.99 | 28 | CR8 |
| 4 | 77 | 0.75 | 0.98 | 27 | CR8 |
| 5 | 83 | 0.74 | 0.97 | 25 | CR8 |
Interfaces
6 interfaces between chains.
- C–D · 1641 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1581 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1004 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 999 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4DXM · Crystal Structure of an ancestral GFP-like 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 4DXM · PDBe 4DXM
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