MolNFT v1 · #82815 · protein
Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2 N140 truncation mutant (resideus 140-408)
3VYO · Probable conserved lipoprotein lpps: “Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2 N140 truncation mutant (resideus…”. X-ray diffraction, 5 pockets (best druggability 0.81). MolNFT v1 #82815 on…
- PDB
- 3VYO
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable conserved lipoprotein lpps
- EC
- 2.3.2.12
- UniProt
- O53223
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable conserved lipoprotein lpps (EC 2.3.2.12) | protein | 261 | 13% helix, 40% strand | O53223 |
| B | Probable conserved lipoprotein lpps (EC 2.3.2.12) | protein | 262 | 12% helix, 40% strand | O53223 |
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 | 199 | 0.81 | 0.95 | 35 | empty |
| 2 | 79 | 0.47 | 0.82 | 19 | empty |
| 3 | 97 | 0.43 | 0.79 | 21 | empty |
| 4 | 99 | 0.41 | 0.77 | 18 | empty |
| 5 | 79 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 833 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3VYO · Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N140 truncation… · 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 3VYO · PDBe 3VYO · UniProt O53223
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