MolNFT v1 · #119227 · protein
Structure of bacterial DNA ligase with small-molecule ligand 1H-indazol-7-amine (AT4213) in an alternate binding site.
5FPO: “Structure of bacterial DNA ligase with small-molecule ligand 1H-indazol-7-amine (AT4213) in an alternate…”. X-ray diffraction, 1 ligand (10L), 4 pockets (best druggability 0.66). MolNFT v1 #119227 on GenesisL1: 3D structure, binding…
- PDB
- 5FPO
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.2, 6.5.1.1
- UniProt
- Q9AIU7
- Ligands
- 10L
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.2, 6.5.1.1) | protein | 305 | 41% helix, 22% strand | Q9AIU7 |
Ligands and binding sites
- 10L · 1H-indazol-7-amine · ligand · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.66 | 0.80 | 50 | 10L |
| 2 | 198 | 0.50 | 0.76 | 37 | empty |
| 3 | 146 | 0.50 | 0.79 | 23 | 10L |
| 4 | 67 | 0.32 | 0.75 | 18 | empty |
Compared structures
- 5FPO · Structure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AIU7 · AlphaFold monomer V2.0 prediction for DNA ligase (Q9AIU7) · 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 Q9AIU7
- Elsewhere: RCSB PDB 5FPO · PDBe 5FPO · UniProt Q9AIU7
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