Research workbench
Crystal structure of LDTMT2, a L,D-transpeptidase from mycobacterium tuberculosis: domain B and C
Analyse Crystal structure of LDTMT2, a L,D-transpeptidase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HUC
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable conserved lipoprotein lpps
- UniProt
- O53223
- Ligands
- NA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable conserved lipoprotein lpps | protein | 261 | 13% helix, 42% strand | O53223 |
| B | Probable conserved lipoprotein lpps | protein | 260 | 12% helix, 40% strand | O53223 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 12 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.77 | 0.86 | 65 | ACT |
| 2 | 90 | 0.43 | 0.79 | 19 | empty |
| 3 | 68 | 0.41 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 837 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4HUC · Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain… · the same entry in another collection · chain A against A, TM-score 1.00
- O53223 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (O53223) · a predicted model of the same protein · chain B 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 4HUC · PDBe 4HUC · UniProt O53223
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