Research workbench
Crystal structure of the rrm domain of S. pombe PUF1 in the P21 space group
Analyse Crystal structure of the rrm domain of S. pombe PUF1 in the P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NX5
- Type
- protein
- Length
- 309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pumilio domain-containing protein C56F2.08C
- UniProt
- O60059
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pumilio domain-containing protein C56F2.08C | protein | 83 | 23% helix, 30% strand | O60059 |
| B | Pumilio domain-containing protein C56F2.08C | protein | 77 | 29% helix, 35% strand | O60059 |
| C | Pumilio domain-containing protein C56F2.08C | protein | 74 | 30% helix, 30% strand | O60059 |
| D | Pumilio domain-containing protein C56F2.08C | protein | 75 | 27% helix, 32% strand | O60059 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
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 | 132 | 0.45 | 0.77 | 28 | empty |
| 2 | 50 | 0.40 | 0.82 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 986 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 706 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 480 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 262 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 231 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NX5 · Crystal structure of the RRM domain of S. pombe Puf1 in the P21 space group · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.94
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 6NX5 · PDBe 6NX5 · UniProt O60059
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