Research workbench
Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic resistance: calcium binding promotes dimer formation
Analyse Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QR7
- Type
- protein
- Length
- 349 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase ldtb
- UniProt
- I6Y9J2
- Ligands
- MLD, DWZ
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase ldtb | protein | 349 | 8% helix, 42% strand | I6Y9J2 |
Ligands and binding sites
- MLD · Glcnac(beta1-4)-murnac(1,6-anhydro)-L-ala-gamma-D-glu-meso-A2PM-D-ala · ligand · chains A
- DWZ · (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.46 | 0.82 | 20 | empty |
| 2 | 124 | 0.43 | 0.76 | 22 | DWZ |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4QR7 · Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and… · the same entry in another collection · chain A against A, TM-score 1.00
- I6Y9J2 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (I6Y9J2) · 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 I6Y9J2
- Elsewhere: RCSB PDB 4QR7 · PDBe 4QR7 · UniProt I6Y9J2
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