MolNFT v1 · #123439 · protein + RNA
Crystal structure of RV2837C complexed with 5'-papa and 5'-AMP
5JJU · Uncharacterized protein RV2837C: “Crystal structure of RV2837C complexed with 5'-papa and 5'-AMP”. X-ray diffraction, 2 ligands (AMP, MN), 2 pockets (best druggability 0.87). MolNFT v1 #123439 on GenesisL1: 3D structure, binding…
- PDB
- 5JJU
- Type
- protein + RNA
- Length
- 652 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein RV2837C; RNA (5'-R(P*AP*A)-3')
- UniProt
- A5U6I9
- Ligands
- AMP, MN
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein RV2837C | protein | 325 | 43% helix, 20% strand | A5U6I9 |
| C | RNA (5'-R(P*AP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains B
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.87 | 0.89 | 101 | AMP |
| 2 | 134 | 0.44 | 0.77 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2041 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5JJU · Crystal structure of Rv2837c complexed with 5'-pApA and 5'-AMP · the same entry in another collection · chain A against A, TM-score 1.00
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 A5U6I9
- Elsewhere: RCSB PDB 5JJU · PDBe 5JJU · UniProt A5U6I9
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