Research workbench
Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2 (LDTMT2) bc-module with faropenem-derived adduct at the active site cysteine-354
Analyse Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LBG
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- UniProt
- O53223
- Ligands
- 3HL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 259 | 13% helix, 41% strand | O53223 |
Ligands and binding sites
- 3HL · (3S)-3-hydroxybutanoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.81 | 0.82 | 101 | empty |
| 2 | 110 | 0.50 | 0.81 | 18 | empty |
| 3 | 164 | 0.47 | 0.76 | 28 | 3HL |
| 4 | 107 | 0.41 | 0.76 | 22 | empty |
| 5 | 103 | 0.40 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1111 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5LBG · Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2)… · the same entry in another collection · chain A against A, TM-score 1.00
- O53223 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (O53223) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O53223
- Elsewhere: RCSB PDB 5LBG · PDBe 5LBG · UniProt O53223
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