MolNFT v1 · #117020 · protein
Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with doripenem adduct
5DVP: “Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 2 with doripenem adduct”. X-ray diffraction, 3 ligands (DRW, POA, SO4), 8 pockets (best druggability 0.70). MolNFT v1 #117020 on GenesisL1: 3D structure, binding…
- PDB
- 5DVP
- Type
- protein
- Length
- 700 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
- I6Y9J2
- Ligands
- DRW, POA, SO4
- Pockets
- 8 · best druggability 0.70
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 | 350 | 9% helix, 44% strand | I6Y9J2 |
Ligands and binding sites
- DRW · (2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- POA · Phosphonoacetaldehyde · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.70 | 0.78 | 41 | empty |
| 2 | 84 | 0.47 | 0.82 | 20 | empty |
| 3 | 190 | 0.43 | 0.73 | 26 | empty |
| 4 | 82 | 0.43 | 0.80 | 21 | empty |
| 5 | 92 | 0.41 | 0.77 | 20 | POA |
Interfaces
1 interface between chains.
- A–B · 439 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DVP · Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct · the same entry in another collection · chain A against A, TM-score 1.00
- I6Y9J2 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (I6Y9J2) · 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 I6Y9J2
- Elsewhere: RCSB PDB 5DVP · PDBe 5DVP · UniProt I6Y9J2
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