MolNFT v1 · #158532 · protein
Crystal structure of the rrm domain of S. pombe PUF1 in the P212121 space group
6NWW · Pumilio domain-containing protein C56F2.08C: “Crystal structure of the rrm domain of S. pombe PUF1 in the P212121 space group”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.32). MolNFT v1 #158532 on GenesisL1: 3D…
- PDB
- 6NWW
- Type
- protein
- Length
- 306 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pumilio domain-containing protein C56F2.08C
- UniProt
- O60059
- Ligands
- CL
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Pumilio domain-containing protein C56F2.08C | protein | 76 | 29% helix, 36% strand | O60059 |
| C | Pumilio domain-containing protein C56F2.08C | protein | 78 | 28% helix, 33% strand | O60059 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, D
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 | 84 | 0.32 | 0.73 | 22 | empty |
| 2 | 73 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 835 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 789 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 127 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NWW · Crystal structure of the RRM domain of S. pombe Puf1 in the P212121 space group · 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 A against A, TM-score 0.89
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 6NWW · PDBe 6NWW · UniProt O60059
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