Research workbench
Crystal structure of a heptameric ring complex of yeast smf in spacegroup P4122
Analyse Crystal structure of a heptameric ring complex of yeast smf in spacegroup P4122 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N9R
- Type
- protein
- Length
- 478 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small nuclear ribonucleoprotein F
- UniProt
- P54999
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G | Small nuclear ribonucleoprotein F | protein | 68 | 9% helix, 57% strand | P54999 |
| B, F | Small nuclear ribonucleoprotein F | protein | 69 | 4% helix, 57% strand | P54999 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.58 | 0.73 | 59 | empty |
| 2 | 69 | 0.34 | 0.76 | 15 | empty |
| 3 | 66 | 0.34 | 0.76 | 15 | empty |
| 4 | 72 | 0.33 | 0.75 | 14 | empty |
| 5 | 69 | 0.32 | 0.75 | 15 | empty |
Interfaces
7 interfaces between chains.
- F–G · 682 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 661 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 621 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 604 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 603 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1N9R · Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122 · the same entry in another collection · chain G against G, TM-score 1.00
- P54999 · AlphaFold monomer V2.0 prediction for small nuclear ribonucleoprotein F (P54999) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P54999
- Elsewhere: RCSB PDB 1N9R · PDBe 1N9R · UniProt P54999
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