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Crystal structure of human fibrillarin in complex with fragment 1 from cocktail soak
Analyse Crystal structure of human fibrillarin in complex with fragment 1 from cocktail… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SE8
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA 2'-O-methyltransferase fibrillarin
- EC
- 2.1.1.-
- UniProt
- P22087
- Ligands
- 8W1
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-) | protein | 228 | 29% helix, 32% strand | P22087 |
Ligands and binding sites
- 8W1 · (5S)-3-methyl-7-(trifluoromethyl)pyrrolo[1,2-a]pyrazin-1(2H)-one · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 8 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.53 | 0.80 | 19 | 8W1, FMT |
| 2 | 142 | 0.50 | 0.79 | 19 | 8W1, FMT |
| 3 | 76 | 0.39 | 0.78 | 14 | empty |
| 4 | 50 | 0.26 | 0.74 | 13 | FMT |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7SE8 · Crystal structure of human Fibrillarin in complex with fragment 1 from cocktail soak · the same entry in another collection · chain A against A, TM-score 1.00
- P22087 · AlphaFold monomer V2.0 prediction for rRNA 2'-O-methyltransferase fibrillarin (P22087) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P22087
- Elsewhere: RCSB PDB 7SE8 · PDBe 7SE8 · UniProt P22087
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