MolNFT v1 · #27549 · protein
Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata
1XMZ · GFP-like chromoprotein FP595: “Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata”. X-ray diffraction, 2 ligands (CRK, NH2), 5 pockets (best druggability 0.75). MolNFT v1 #27549 on…
- 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
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