MolNFT v1 · #25456 · protein
Crystal structure of the ligase domain from M. tuberculosis ligd at 2.4A
1VS0 · Putative DNA ligase-like protein RV0938/MT0965: “Crystal structure of the ligase domain from M. tuberculosis ligd at 2.4A”. X-ray diffraction, 3 ligands (ZN, MG, CL), 2 pockets (best druggability 0.33). MolNFT v1 #25456 on…
- 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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