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Crystallographic structure of L,D-transpeptidase 2 from mycobacterium tuberculosis
Analyse Crystallographic structure of L,D-transpeptidase 2 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KEM
- Type
- protein
- Length
- 527 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
- 0JC, DGL, 6CL, PT
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 258 | 12% helix, 41% strand | I6Y9J2 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 269 | 12% helix, 40% strand | I6Y9J2 |
Ligands and binding sites
- 0JC · Di-mu-iodobis(ethylenediamine)diplatinum(II) · ligand · 8 copies · chains A, B
- DGL · D-glutamic acid · ligand · chains A, B
- 6CL · 6-carboxylysine · ligand · chains A
- PT · Platinum (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.76 | 0.86 | 63 | DGL, 6CL |
| 2 | 100 | 0.53 | 0.84 | 18 | 0JC |
| 3 | 80 | 0.42 | 0.80 | 18 | 0JC |
Interfaces
1 interface between chains.
- A–B · 824 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7KEM · Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis · 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 0.99
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 I6Y9J2
- Elsewhere: RCSB PDB 7KEM · PDBe 7KEM · UniProt I6Y9J2
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