Research workbench
Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation a
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
- 5DZJ
- Type
- protein
- Length
- 700 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
- 6B7
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% 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 | 349 | 9% helix, 43% strand | I6Y9J2 |
Ligands and binding sites
- 6B7 · (2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.51 | 0.77 | 26 | 6B7 |
| 2 | 165 | 0.50 | 0.77 | 30 | 6B7 |
| 3 | 81 | 0.46 | 0.82 | 20 | empty |
| 4 | 80 | 0.45 | 0.81 | 21 | empty |
| 5 | 59 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DZJ · 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 5DZJ · PDBe 5DZJ · UniProt I6Y9J2
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