Research workbench
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
- 4UF4
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase A1
- EC
- 3.4.17.1
- UniProt
- P15085
- Ligands
- O2V, ZN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 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 | 38% helix, 19% strand | P15085 |
Ligands and binding sites
- O2V · (2S)-4-methyl-2-[(1R)-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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.74 | 0.83 | 67 | O2V |
| 2 | 63 | 0.71 | 0.97 | 22 | O2V |
| 3 | 407 | 0.68 | 0.81 | 45 | empty |
| 4 | 315 | 0.59 | 0.77 | 44 | empty |
| 5 | 117 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 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 4UF4 · PDBe 4UF4 · UniProt P15085
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.