Research workbench
Crystal structure of bovine pancreatic carboxypeptidase a complexed with aminocarbonylphenylalanine at 1.75 a
Analyse Crystal structure of bovine pancreatic carboxypeptidase a complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDU
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase a
- EC
- 3.4.17.1
- UniProt
- P00730
- Ligands
- ING, ZN
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Carboxypeptidase a (EC 3.4.17.1) | protein | 307 | 38% helix, 18% strand | P00730 |
Ligands and binding sites
- ING · D-[(amino)carbonyl]phenylalanine · ligand · 4 copies · chains A, B, D, E
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, E
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 | 784 | 0.81 | 0.84 | 81 | ING |
| 2 | 1160 | 0.80 | 0.81 | 102 | ING |
| 3 | 137 | 0.64 | 0.87 | 26 | ING |
| 4 | 132 | 0.63 | 0.87 | 24 | ING |
| 5 | 117 | 0.50 | 0.81 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–E · 483 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 221 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1HDU · Crystal structure of bovine pancreatic carboxypeptidase A complexed with… · the same entry in another collection · chain E against E, TM-score 1.00
- P00730 · AlphaFold monomer V2.0 prediction for carboxypeptidase A1 (P00730) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P00730
- Elsewhere: RCSB PDB 1HDU · PDBe 1HDU · UniProt P00730
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