Research workbench
Crystal structure of activated porcine pancreatic carboxypeptidase B (3-aminomethyl-phenyl)-[((R)-1- benzyloxycarbonylamino-2-methyl-propyl)-hydroxy- phosphinoyloxy]-acetic 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
- 2PJ1
- Type
- protein
- Length
- 914 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
- 578, ZN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B (EC 3.4.17.2) | protein | 304 | 38% helix, 17% strand | P09955 |
| B, C | Carboxypeptidase B (EC 3.4.17.2) | protein | 305 | 39% helix, 17% strand | P09955 |
Ligands and binding sites
- 578 · (5R,6S,8S)-8-[3-(aminomethyl)phenyl]-6-hydroxy-5-isopropyl-3-oxo-1-phenyl-2,7-dioxa-4-aza-6-phosphanonan-9-oic acid 6-oxide · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.65 | 0.78 | 53 | 578 |
| 2 | 99 | 0.63 | 0.89 | 22 | 578 |
| 3 | 120 | 0.61 | 0.87 | 25 | 578 |
| 4 | 125 | 0.43 | 0.77 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 459 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 219 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 2PJ1 · PDBe 2PJ1 · UniProt P09955
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