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Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with a thiirane mechanism-based inhibitor
Analyse Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with a thiirane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OM9
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens
- Molecule
- Carboxypeptidase A1
- EC
- 3.4.17.1
- UniProt
- P15085
- Ligands
- O2S, ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase A1 (EC 3.4.17.1) | protein | 396 | 40% helix, 18% strand | P15085 |
| B | Carboxypeptidase A1 (EC 3.4.17.1) | protein | 392 | 39% helix, 19% strand | P15085 |
Ligands and binding sites
- O2S · (2~{R})-4-methyl-2-[(1~{S})-1-sulfanylethyl]pentanoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.74 | 0.83 | 68 | O2S |
| 2 | 57 | 0.70 | 0.98 | 19 | O2S |
| 3 | 406 | 0.68 | 0.81 | 47 | empty |
| 4 | 396 | 0.62 | 0.77 | 59 | empty |
| 5 | 115 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 5OM9 · Crystal structure of the human carboxypeptidase A1 in complex with a thiirane… · the same entry in another collection · chain A against A, TM-score 1.00
- P15085 · AlphaFold monomer V2.0 prediction for carboxypeptidase A1 (P15085) · 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 P15085
- Elsewhere: RCSB PDB 5OM9 · PDBe 5OM9 · UniProt P15085
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