Research workbench
Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis
Analyse Structural basis for domain rotation during adenylation of active site K123 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KKV
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.56
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- DNA ligase A
- EC
- 6.5.1.2
- UniProt
- P9WNV1
- Ligands
- DKR, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.56 · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase A (EC 6.5.1.2) | protein | 321 | 36% helix, 22% strand | P9WNV1 |
Ligands and binding sites
- DKR · N-[(4-methylphenyl)methyl]-1H-pyrrole-2-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.72 | 0.81 | 64 | SO4 |
| 2 | 156 | 0.44 | 0.75 | 28 | empty |
| 3 | 52 | 0.35 | 0.78 | 13 | DKR |
Compared structures
- 6KKV · Structural basis for domain rotation during adenylation of active site K123 and fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WNV1 · AlphaFold monomer V2.0 prediction for DNA ligase a (P9WNV1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P9WNV1
- Elsewhere: RCSB PDB 6KKV · PDBe 6KKV · UniProt P9WNV1
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