Research workbench
Complex of D-ALA:D-ala ligase with ADP and a phosphoryl phosphonate
Analyse Complex of D-ALA:D-ala ligase with ADP and a phosphoryl phosphonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IOV
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ALA\:D-ala ligase
- EC
- 6.3.2.4
- UniProt
- P07862
- Ligands
- ADP, POB, MG
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-ALA\:D-ala ligase (EC 6.3.2.4) | protein | 306 | 33% helix, 22% strand | P07862 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- POB · 2-[(1-amino-ethyl)-phosphate-phosphinoyloxy]-butyric acid · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.78 | 0.92 | 45 | MG, ADP, POB |
Compared structures
- 1IOV · Complex of D-ALA:D-ala ligase with ADP and a phosphoryl phosphonate · the same entry in another collection · chain A against A, TM-score 1.00
- P07862 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase B (P07862) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P07862
- Elsewhere: RCSB PDB 1IOV · PDBe 1IOV · UniProt P07862
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