Research workbench
Crystal structure of human fibrillarin in complex with compound 1A
Analyse Crystal structure of human fibrillarin in complex with compound 1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SEC
- Type
- protein
- Length
- 452 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
- 8WP
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-) | protein | 227 | 29% helix, 32% strand | P22087 |
| B | RRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-) | protein | 225 | 29% helix, 32% strand | P22087 |
Ligands and binding sites
- 8WP · 2-[(8S)-4-oxo-2-(trifluoromethyl)-4,5-dihydropyrazolo[1,5-a]pyrazin-6-yl]acetamide · 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.59 | 0.79 | 36 | FMT, 8WP, DMS |
| 2 | 235 | 0.58 | 0.79 | 36 | FMT, 8WP, DMS |
| 3 | 129 | 0.52 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 677 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7SEC · Crystal structure of human Fibrillarin in complex with compound 1a · 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 7SEC · PDBe 7SEC · UniProt P22087
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