Research workbench
mycobacterial DNA ligase D complexed with ATP and Mg
Analyse mycobacterial DNA ligase D complexed with ATP and Mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NHZ
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Mycobacterium tuberculosis
- Molecule
- ATP-dependent DNA ligase
- EC
- 6.5.1.1
- UniProt
- A0A0T9BTX3
- Ligands
- ATP, MG
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA ligase (EC 6.5.1.1) | protein | 303 | 18% helix, 36% strand | A0A0T9BTX3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.64 | 0.80 | 29 | ATP, MG |
| 2 | 229 | 0.64 | 0.82 | 36 | empty |
| 3 | 50 | 0.32 | 0.78 | 13 | empty |
| 4 | 57 | 0.31 | 0.76 | 15 | empty |
Compared structures
- 6NHZ · Mycobacterial DNA ligase D complexed with ATP and mg · 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 A0A0T9BTX3
- Elsewhere: RCSB PDB 6NHZ · PDBe 6NHZ · UniProt A0A0T9BTX3
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