MolNFT v1 · #154522 · protein
Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis
6KDU · DNA ligase a: “Structural basis for domain rotation during adenylation of active site K123 and fragment library screening…”. X-ray diffraction, 3 ligands (AMP, NMN, SO4), 2 pockets (best druggability 0.73). MolNFT v1 #154522 on…
- PDB
- 6KDU
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase a
- EC
- 6.5.1.2
- UniProt
- P9WNV1
- Ligands
- AMP, NMN, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase a (EC 6.5.1.2) | protein | 321 | 40% helix, 22% strand | P9WNV1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- NMN · Beta-nicotinamide ribose monophosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.73 | 0.82 | 57 | AMP, SO4 |
| 2 | 115 | 0.40 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6KDU · 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 6KDU · PDBe 6KDU · UniProt P9WNV1
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