Research workbench
Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata
Analyse Crystal structure of the dark state of kindling fluorescent protein kfp from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XMZ
- Type
- protein
- Length
- 455 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like chromoprotein FP595
- Ligands
- CRK, NH2
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GFP-like chromoprotein FP595 | protein | 224 | 6% helix, 54% strand | — |
| B | GFP-like chromoprotein FP595 | protein | 231 | 7% helix, 52% strand | — |
Ligands and binding sites
- CRK · 4-{(Z)-[2-[3-(methylsulfanyl)propanoyl]-5-oxo-1-(2-oxoethyl)-1,5-dihydro-4H-imidazol-4-ylidene]methyl}benzenolate · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.75 | 0.97 | 26 | CRK |
| 2 | 75 | 0.74 | 0.98 | 22 | CRK |
| 3 | 94 | 0.44 | 0.79 | 15 | empty |
| 4 | 77 | 0.40 | 0.79 | 17 | empty |
| 5 | 59 | 0.33 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 992 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (additive adduct, covalent ligand).
Compared structures
- 1XMZ · Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia… · the same entry in another collection · chain B against B, TM-score 0.29
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1XMZ · PDBe 1XMZ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.