MolNFT v1 · #102399 · protein
Crystal structure of RNase as from M tuberculosis in complex with ump
4OKK · 3'-5' exoribonuclease RV2179C/MT2234.1: “Crystal structure of RNase as from M tuberculosis in complex with ump”. X-ray diffraction, 2 ligands (U5P, MG), 3 pockets (best druggability 0.61). MolNFT v1 #102399 on GenesisL1: 3D…
- PDB
- 4OKK
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3'-5' exoribonuclease RV2179C/MT2234.1
- EC
- 3.1.13.-
- UniProt
- L7N5T0
- Ligands
- U5P, MG
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3'-5' exoribonuclease RV2179C/MT2234.1 (EC 3.1.13.-) | protein | 160 | 37% helix, 21% strand | L7N5T0 |
| B | 3'-5' exoribonuclease RV2179C/MT2234.1 (EC 3.1.13.-) | protein | 158 | 35% helix, 22% strand | L7N5T0 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.61 | 0.76 | 38 | U5P, MG |
| 2 | 280 | 0.56 | 0.76 | 31 | U5P, MG |
| 3 | 109 | 0.43 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1284 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4OKK · Crystal structure of RNase AS from M tuberculosis in complex with UMP · 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 L7N5T0
- Elsewhere: RCSB PDB 4OKK · PDBe 4OKK · UniProt L7N5T0
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