MolNFT v1 · #82421 · protein
Crystal structure of bacd, an L-amino acid dipeptide ligase from bacillus subtilis
3VMM · Alanine-anticapsin ligase bacd: “Crystal structure of bacd, an L-amino acid dipeptide ligase from bacillus subtilis”. X-ray diffraction, 3 ligands (ADP, P0D, MG), 3 pockets (best druggability 0.81). MolNFT v1 #82421 on GenesisL1: 3D…
- PDB
- 3VMM
- Type
- protein
- Length
- 471 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, P0D, MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine-anticapsin ligase bacd (EC 6.3.2.28) | protein | 471 | 35% helix, 26% strand | P39641 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- P0D · (2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid · 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 | 949 | 0.81 | 0.82 | 88 | MG, ADP, P0D |
| 2 | 98 | 0.33 | 0.73 | 18 | empty |
| 3 | 61 | 0.30 | 0.74 | 16 | empty |
Compared structures
- 3VMM · Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis · 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 3VMM · PDBe 3VMM · UniProt P39641
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