MolNFT v1 · #88610 · protein
Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant bacterium
4D05: “Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant bacterium”. X-ray diffraction, 3 ligands (AMP, MG, SO4), 3 pockets (best druggability 0.66). MolNFT v1 #88610 on GenesisL1: 3D structure…
- PDB
- 4D05
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA ligase
- Ligands
- AMP, MG, SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA ligase | protein | 258 | 23% helix, 34% strand | — |
| B | ATP-dependent DNA ligase | protein | 249 | 21% helix, 33% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.66 | 0.84 | 30 | AMP, MG |
| 2 | 225 | 0.62 | 0.82 | 36 | SO4, AMP |
| 3 | 80 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 546 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 4D05 · Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant… · 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
- Elsewhere: RCSB PDB 4D05 · PDBe 4D05
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