MolNFT v1 · #158028 · protein
Mycobacterial DNA ligase D complexed with ATP and mes
6NHX · ATP-dependent DNA ligase: “Mycobacterial DNA ligase D complexed with ATP and mes”. X-ray diffraction, 1 ligand (ATP), 2 pockets (best druggability 0.70). MolNFT v1 #158028 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6NHX
- Type
- protein
- Length
- 301 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA ligase
- EC
- 6.5.1.1
- UniProt
- A0A0T9BTX3
- Ligands
- ATP
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA ligase (EC 6.5.1.1) | protein | 301 | 21% helix, 38% strand | A0A0T9BTX3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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 | 456 | 0.70 | 0.81 | 43 | ATP, MES |
| 2 | 107 | 0.37 | 0.74 | 24 | empty |
Compared structures
- 6NHX · mycobacterial DNA ligase D complexed with ATP and MES · 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 6NHX · PDBe 6NHX · UniProt A0A0T9BTX3
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