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Crystal structure of bacillus subtilis ywfe, an L-amino acid ligase, with bound ADP-mg-ala
Analyse Crystal structure of bacillus subtilis ywfe, an L-amino acid ligase, with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WO0
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine-anticapsin ligase bacd
- EC
- 6.3.2.28
- UniProt
- P39641
- Ligands
- ADP, ALA, MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine-anticapsin ligase bacd (EC 6.3.2.28) | protein | 465 | 37% helix, 25% strand | P39641 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALA · Alanine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.81 | 0.82 | 76 | ADP, MG, ALA |
| 2 | 109 | 0.37 | 0.74 | 20 | empty |
| 3 | 54 | 0.28 | 0.74 | 11 | empty |
Compared structures
- 3WO0 · Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala · the same entry in another collection · chain A against A, TM-score 1.00
- P39641 · AlphaFold monomer V2.0 prediction for alanine--anticapsin ligase (P39641) · a predicted model of the same protein · 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 P39641
- Elsewhere: RCSB PDB 3WO0 · PDBe 3WO0 · UniProt P39641
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