Research workbench
Crystal structure of LDTMT2 from mycobacterium tuberculosis bound to ebselen
Analyse Crystal structure of LDTMT2 from mycobacterium tuberculosis bound to ebselen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RRM
- Type
- protein
- Length
- 702 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
- 9JT, NH4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 351 | 9% helix, 44% strand | O53223 |
Ligands and binding sites
- 9JT · ~{N}-phenyl-2-selanyl-benzamide · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.71 | 0.77 | 51 | NH4 |
| 2 | 186 | 0.51 | 0.77 | 31 | 9JT |
| 3 | 95 | 0.49 | 0.82 | 21 | NH4 |
| 4 | 149 | 0.46 | 0.76 | 24 | 9JT |
| 5 | 55 | 0.45 | 0.84 | 21 | NH4 |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6RRM · Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen · the same entry in another collection · chain B against B, 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 6RRM · PDBe 6RRM · UniProt O53223
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