Research workbench
Crystal structure of activated porcine pancreatic carboxypeptidase B 2-(3-aminomethyl-phenyl)-3-{[1-((S)-2- benzyloxycarbonylamino-3-phenyl-propane-1-sulfonylamino)-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
- 2PJB
- Type
- protein
- Length
- 913 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
- 983, ZN
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Carboxypeptidase B (EC 3.4.17.2) | protein | 304 | 39% helix, 18% strand | P09955 |
| B | Carboxypeptidase B (EC 3.4.17.2) | protein | 305 | 38% helix, 17% strand | P09955 |
Ligands and binding sites
- 983 · (5S,9R,10R,12S)-12-[3-(aminomethyl)phenyl]-5-benzyl-10-hydroxy-9-isopropyl-3-oxo-1-phenyl-2-oxa-7-thia-4,8-diaza-10-phosphatridecan-13-oic acid 7,7,10-trioxide · 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
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 | 308 | 0.61 | 0.79 | 47 | 983 |
| 2 | 177 | 0.56 | 0.81 | 28 | 983 |
| 3 | 271 | 0.55 | 0.76 | 27 | empty |
| 4 | 140 | 0.55 | 0.82 | 24 | 983 |
| 5 | 56 | 0.28 | 0.74 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 468 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 2 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 2PJB · PDBe 2PJB · UniProt P09955
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