Research workbench
Crystal structure of the mycobacterium tuberculosis L,D- transpeptidase-2 (LDTMT2) bc-module with thionitrobenzoate (tnb) 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
- 5LB1
- Type
- protein
- Length
- 511 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
- I6Y9J2
- Ligands
- MNB
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 258 | 12% helix, 40% strand | I6Y9J2 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 253 | 12% helix, 41% strand | I6Y9J2 |
Ligands and binding sites
- MNB · 5-mercapto-2-nitro-benzoic acid · 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 | 991 | 0.77 | 0.79 | 103 | MNB |
| 2 | 437 | 0.63 | 0.77 | 45 | MNB |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5LB1 · 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
- 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 5LB1 · PDBe 5LB1 · UniProt I6Y9J2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.