MolNFT v1 · #116983 · protein
Crystal structure of LDTMT2 in complex with faropenem adduct
5DUJ · L,D-transpeptidase 2: “Crystal structure of LDTMT2 in complex with faropenem adduct”. X-ray diffraction, 2 ligands (DGF, SO4), 7 pockets (best druggability 0.49). MolNFT v1 #116983 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DUJ
- Type
- protein
- Length
- 701 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
- DGF, SO4
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 351 | 9% helix, 44% strand | O53223 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 350 | 9% helix, 44% strand | O53223 |
Ligands and binding sites
- DGF · (2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.49 | 0.82 | 23 | empty |
| 2 | 50 | 0.48 | 0.87 | 16 | empty |
| 3 | 73 | 0.46 | 0.82 | 18 | empty |
| 4 | 102 | 0.41 | 0.76 | 18 | DGF |
| 5 | 98 | 0.40 | 0.77 | 19 | DGF |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 5DUJ · PDBe 5DUJ · UniProt O53223
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