Research workbench
Crystal structure of the bacillus subtilis PBP4A, and its complex with a peptidoglycan mimetic peptide.
Analyse Crystal structure of the bacillus subtilis PBP4A, and its complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J9P
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase dacc
- EC
- 3.4.16.4
- UniProt
- P39844
- Ligands
- REZ, DAL
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-alanyl-D-alanine carboxypeptidase dacc (EC 3.4.16.4) | protein | 458 | 31% helix, 26% strand | P39844 |
Ligands and binding sites
- REZ · (2R)-2-amino-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoic acid · ligand · 2 copies · chains A, B
- DAL · D-alanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.58 | 0.78 | 51 | REZ, DAL |
| 2 | 222 | 0.51 | 0.76 | 39 | REZ, DAL |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2J9P · Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan… · the same entry in another collection · chain A against A, TM-score 1.00
- P39844 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacc (P39844) · 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 P39844
- Elsewhere: RCSB PDB 2J9P · PDBe 2J9P · UniProt P39844
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