Research workbench
Crystal structure of L,D-transpeptidase 3 from mycobacterium tuberculosis in complex with a faropenem-derived adduct
Analyse Crystal structure of L,D-transpeptidase 3 from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D51
- Type
- protein
- Length
- 235 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable L,D-transpeptidase 3
- EC
- 2.3.2.-
- UniProt
- O06825
- Ligands
- ACE, CA
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable L,D-transpeptidase 3 (EC 2.3.2.-) | protein | 235 | 12% helix, 41% strand | O06825 |
Ligands and binding sites
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 | 138 | 0.51 | 0.79 | 28 | ACE |
| 2 | 118 | 0.48 | 0.80 | 21 | empty |
| 3 | 78 | 0.33 | 0.74 | 24 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6D51 · Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O06825 · AlphaFold monomer V2.0 prediction for probable L,D-transpeptidase 3 (O06825) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O06825
- Elsewhere: RCSB PDB 6D51 · PDBe 6D51 · UniProt O06825
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