Research workbench
Crystal structure of snap-tag labeled with a benzyl- tetramethylrhodamine fluorophore
Analyse Crystal structure of snap-tag labeled with a benzyl- tetramethylrhodamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y8P
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O6-alkylguanine-DNA alkyltransferase mutant
- UniProt
- E5BBQ0
- Ligands
- OGQ, ZN
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O6-alkylguanine-DNA alkyltransferase mutant | protein | 158 | 41% helix, 16% strand | E5BBQ0 |
Ligands and binding sites
- OGQ · [9-[2-carboxy-5-[(4-methylphenyl) methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.47 | 0.80 | 14 | empty |
| 2 | 51 | 0.29 | 0.76 | 15 | EDO |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6Y8P · Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore · 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 E5BBQ0
- Elsewhere: RCSB PDB 6Y8P · PDBe 6Y8P · UniProt E5BBQ0
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