MolNFT v1 · #82816 · protein
Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2-N140 adduct with meropenem
3VYP · Probable conserved lipoprotein lpps: “Crystal structure of mycobacterium tuberculosis L,D-transpeptidase LDTMT2-N140 adduct with meropenem”. X-ray diffraction, 1 ligand (MXR), 4 pockets (best druggability 0.74). MolNFT v1 #82816 on…
- PDB
- 3VYP
- Type
- protein
- Length
- 532 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
- Ligands
- MXR
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable conserved lipoprotein lpps (EC 2.3.2.12) | protein | 268 | 12% helix, 38% strand | O53223 |
| B | Probable conserved lipoprotein lpps (EC 2.3.2.12) | protein | 264 | 13% helix, 39% strand | O53223 |
Ligands and binding sites
- MXR · (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.74 | 0.77 | 79 | MXR |
| 2 | 157 | 0.45 | 0.76 | 28 | MXR |
| 3 | 85 | 0.44 | 0.81 | 19 | empty |
| 4 | 67 | 0.39 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3VYP · Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2-N140 adduct… · 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 A against A, TM-score 0.96
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 3VYP · PDBe 3VYP · UniProt O53223
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