MolNFT v1 · #134619 · protein
Structural analysis reveals the flexible C-terminus of NOP15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate
5T9P · Ribosome biogenesis protein 15: “Structural analysis reveals the flexible C-terminus of NOP15 undergoes rearrangement to recognize a…”. X-ray diffraction, 2 ligands (SO4, CL), 4 pockets (best druggability 0.70). MolNFT v1 #134619 on…
- PDB
- 5T9P
- Type
- protein
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome biogenesis protein 15
- UniProt
- P53927
- Ligands
- SO4, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ribosome biogenesis protein 15 | protein | 105 | 30% helix, 33% strand | P53927 |
| C | Ribosome biogenesis protein 15 | protein | 106 | 28% helix, 33% strand | P53927 |
| A | Ribosome biogenesis protein 15 | protein | 97 | 25% helix, 36% strand | P53927 |
| D | Ribosome biogenesis protein 15 | protein | 91 | 27% helix, 41% strand | P53927 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains B, A, C, D
- CL · Chloride ion · ion · 7 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.70 | 0.85 | 31 | empty |
| 2 | 123 | 0.46 | 0.78 | 28 | empty |
| 3 | 115 | 0.37 | 0.74 | 23 | CL |
| 4 | 65 | 0.32 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–A · 894 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 893 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5T9P · Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to… · the same entry in another collection · chain D against D, TM-score 1.00
- P53927 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein 15 (P53927) · a predicted model of the same protein · chain D 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 P53927
- Elsewhere: RCSB PDB 5T9P · PDBe 5T9P · UniProt P53927
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