Research workbench
Crystal structure of mycobacterium tuberculosis D,D-peptidase RV3330 in complex with meropenem
Analyse Crystal structure of mycobacterium tuberculosis D,D-peptidase RV3330 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PPR
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein DACB1
- UniProt
- O53380
- Ligands
- MER
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein DACB1 | protein | 300 | 33% helix, 22% strand | O53380 |
Ligands and binding sites
- MER · (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.36 | 0.75 | 26 | MER |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4PPR · Crystal structure of Mycobacterium tuberculosis D,D-peptidase Rv3330 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O53380 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase DACB1 (O53380) · 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 O53380
- Elsewhere: RCSB PDB 4PPR · PDBe 4PPR · UniProt O53380
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