Research workbench
Crystal structure of the ligase domain from M. tuberculosis ligd at 2.4A
Analyse Crystal structure of the ligase domain from M. tuberculosis ligd at 2.4A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VS0
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA ligase-like protein RV0938/MT0965
- UniProt
- P71571
- Ligands
- ZN, MG, CL
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative DNA ligase-like protein RV0938/MT0965 | protein | 299 | 22% helix, 36% strand | P71571 |
| B | Putative DNA ligase-like protein RV0938/MT0965 | protein | 305 | 22% helix, 37% strand | P71571 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.33 | 0.76 | 12 | empty |
| 2 | 55 | 0.31 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered, nonstandard).
Compared structures
- 1VS0 · Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A · 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 P71571
- Elsewhere: RCSB PDB 1VS0 · PDBe 1VS0 · UniProt P71571
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