Research workbench
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210
Analyse Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E1I
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.003
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- UniProt
- I6Y9J2
- Ligands
- 6B8, NA
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · resolution 2.003 · 2 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 351 | 9% helix, 44% strand | I6Y9J2 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 350 | 9% helix, 43% strand | I6Y9J2 |
Ligands and binding sites
- 6B8 · (2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
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 | 179 | 0.51 | 0.77 | 26 | 6B8 |
| 2 | 84 | 0.49 | 0.83 | 20 | empty |
| 3 | 86 | 0.44 | 0.80 | 20 | empty |
| 4 | 161 | 0.43 | 0.75 | 30 | empty |
| 5 | 110 | 0.41 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 533 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5E1I · Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug… · 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 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 I6Y9J2
- Elsewhere: RCSB PDB 5E1I · PDBe 5E1I · UniProt I6Y9J2
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