Research workbench
Crystal structure of the pum-hd domain of S. pombe PUF1 in complex with RNA
Analyse Crystal structure of the pum-hd domain of S. pombe PUF1 in complex with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NY5
- Type
- protein + RNA
- Length
- 769 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pumilio domain-containing protein C56F2.08C; RNA…
- UniProt
- O60059
- Ligands
- MG, SO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pumilio domain-containing protein C56F2.08C | protein | 386 | 69% helix, 0% strand | O60059 |
| B | Pumilio domain-containing protein C56F2.08C | protein | 370 | 71% helix, 0% strand | O60059 |
| C | RNA (5'-R(P*UP*UP*AP*AP*UP*AP*AP*CP*UP*UP*AP*AP*U)-3') | rna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.52 | 0.75 | 28 | empty |
| 2 | 244 | 0.52 | 0.76 | 24 | empty |
| 3 | 89 | 0.43 | 0.78 | 14 | empty |
| 4 | 59 | 0.30 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1047 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 597 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6NY5 · Crystal structure of the PUM-HD domain of S. pombe Puf1 in complex with RNA · the same entry in another collection · chain A against A, TM-score 1.00
- O60059 · AlphaFold monomer V2.0 prediction for pumilio domain-containing protein C56F2.08C (O60059) · 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 O60059
- Elsewhere: RCSB PDB 6NY5 · PDBe 6NY5 · UniProt O60059
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