Research workbench
Crystal structure of PHORPP38 bound to a K-turn in P12.1 helix
Analyse Crystal structure of PHORPP38 bound to a K-turn in P12.1 helix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y7M
- Type
- protein + RNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L7AE; RNA (52-mer)
- UniProt
- P62009
- Ligands
- GTP, SO4
- Pockets
- 4 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 50S ribosomal protein L7AE | protein | 125 | 51% helix, 15% strand | P62009 |
| B, D | RNA (52-mer) | rna | 51 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.36 | 0.74 | 21 | empty |
| 2 | 92 | 0.34 | 0.75 | 17 | empty |
| 3 | 94 | 0.31 | 0.73 | 17 | SO4 |
| 4 | 85 | 0.30 | 0.74 | 13 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 647 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 640 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 604 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 597 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5Y7M · Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix · the same entry in another collection · chain A against A, TM-score 1.00
- P62009 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (P62009) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P62009
- Elsewhere: RCSB PDB 5Y7M · PDBe 5Y7M · UniProt P62009
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