Research workbench
Crystal structure of mycobacterium tuberculosis VAPC20 (RV2549C), sarcin-ricin loop cleaving toxin
Analyse Crystal structure of mycobacterium tuberculosis VAPC20 (RV2549C), sarcin-ricin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZF
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA-specific endonuclease VAPC20
- EC
- 3.1.-.-
- UniProt
- P0DMV7
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA-specific endonuclease VAPC20 (EC 3.1.-.-) | protein | 130 | 55% helix, 12% strand | P0DMV7 |
| B | 23S rRNA-specific endonuclease VAPC20 (EC 3.1.-.-) | protein | 131 | 55% helix, 14% strand | P0DMV7 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.65 | 0.79 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 1234 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5WZF · Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop… · the same entry in another collection · chain A against A, TM-score 1.00
- P0DMV7 · AlphaFold monomer V2.0 prediction for 23S rRNA-specific endonuclease VAPC20 (P0DMV7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0DMV7
- Elsewhere: RCSB PDB 5WZF · PDBe 5WZF · UniProt P0DMV7
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