Research workbench
Crystal structure of the nerve agent degrading organophosphate ANHYDROLASE/PROLIDASE in complex with inhibitors
Analyse Crystal structure of the nerve agent degrading organophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L24
- Type
- protein
- Length
- 1,259 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro dipeptidase
- EC
- 3.4.13.9, 3.1.8.2, 3.1.8.1
- UniProt
- Q44238
- Ligands
- GOA, MN
- Pockets
- 18 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidase (EC 3.4.13.9, 3.1.8.2, 3.1.8.1) | protein | 425 | 41% helix, 18% strand | Q44238 |
| B, C | Xaa-pro dipeptidase (EC 3.4.13.9, 3.1.8.2, 3.1.8.1) | protein | 417 | 41% helix, 18% strand | Q44238 |
Ligands and binding sites
- GOA · Glycolic acid · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.62 | 0.73 | 66 | empty |
| 2 | 415 | 0.59 | 0.75 | 48 | empty |
| 3 | 349 | 0.56 | 0.75 | 40 | empty |
| 4 | 204 | 0.46 | 0.74 | 27 | empty |
| 5 | 149 | 0.45 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 450 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3L24 · Crystal Structure of the Nerve Agent Degrading Organophosphate Anhydrolase/Prolidase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q44238 · AlphaFold monomer V2.0 prediction for xaa-pro dipeptidase (Q44238) · 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 Q44238
- Elsewhere: RCSB PDB 3L24 · PDBe 3L24 · UniProt Q44238
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