MolNFT v1 · #171704 · protein
Crystal structure of eukaryotic fibrillarin with NOP56 N-terminal domain
6ZDT · RRNA 2'-O-methyltransferase fibrillarin: “Crystal structure of eukaryotic fibrillarin with NOP56 N-terminal domain”. X-ray diffraction, 3 pockets (best druggability 0.50). MolNFT v1 #171704 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ZDT
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA 2'-O-methyltransferase fibrillarin; Nucleolar protein 56
- EC
- 2.1.1.-
- UniProt
- P15646, Q12460
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-) | protein | 231 | 28% helix, 33% strand | P15646 |
| B | Nucleolar protein 56 | protein | 166 | 50% helix, 17% strand | Q12460 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.50 | 0.80 | 27 | empty |
| 2 | 187 | 0.44 | 0.74 | 26 | empty |
| 3 | 77 | 0.41 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1582 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6ZDT · Crystal structure of eukaryotic Fibrillarin with Nop56 N-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
- P15646 · AlphaFold monomer V2.0 prediction for rRNA 2'-O-methyltransferase fibrillarin (P15646) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q12460 · AlphaFold monomer V2.0 prediction for nucleolar protein 56 (Q12460) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P15646
- Every structure of UniProt Q12460
- Elsewhere: RCSB PDB 6ZDT · PDBe 6ZDT · UniProt P15646 · UniProt Q12460
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