MolNFT v1 · #158030 · protein
Mycobacterial DNA ligase D complexed with ATP and mg
6NHZ · ATP-dependent DNA ligase: “Mycobacterial DNA ligase D complexed with ATP and mg”. X-ray diffraction, 2 ligands (ATP, MG), 4 pockets (best druggability 0.64). MolNFT v1 #158030 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6NHZ
- Type
- protein
- Length
- 303 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, MG
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 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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