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Crystal structure of activated porcine pancreatic carboxypeptidase B 2-(3-aminomethyl-phenyl)-3-[((R)-1- benzenesulfonylamino-2-methyl-propyl)-hydroxy-phosphinoyl]- propionic acid complex
Analyse Crystal structure of activated porcine pancreatic carboxypeptidase B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PJ7
- Type
- protein
- Length
- 912 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B
- EC
- 3.4.17.2
- UniProt
- P09955
- Ligands
- 235, ZN
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Carboxypeptidase B (EC 3.4.17.2) | protein | 304 | 39% helix, 18% strand | P09955 |
Ligands and binding sites
- 235 · (2S)-2-[3-(aminomethyl)phenyl]-3-[(R)-hydroxy{(1r)-2-methyl-1-[(phenylsulfonyl)amino]propyl}phosphoryl]propanoic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.63 | 0.89 | 21 | 235 |
| 2 | 129 | 0.63 | 0.87 | 23 | 235 |
| 3 | 130 | 0.62 | 0.86 | 24 | 235 |
| 4 | 299 | 0.54 | 0.75 | 32 | empty |
| 5 | 119 | 0.41 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 457 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 189 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
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 P09955
- Elsewhere: RCSB PDB 2PJ7 · PDBe 2PJ7 · UniProt P09955
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