Research workbench
Crystal structure of activated porcine pancreatic carboxypeptidase B 3-{[(R)-1-((S)-2-benzyloxycarbonylamino- 3-phenyl-propionylamino)-2-methyl-propyl]-hydroxy- phosphinoyl}-2-(3-guanidino-phenyl)-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
- 2PJA
- 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
- 33Z, ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Carboxypeptidase B (EC 3.4.17.2) | protein | 304 | 38% helix, 17% strand | P09955 |
Ligands and binding sites
- 33Z · (2S)-2-(3-{[amino(imino)methyl]amino}phenyl)-3-[(R)-[(1R)-1-({N-[(benzyloxy)carbonyl]-L-phenylalanyl}amino)-2-methylpropyl](hydroxy)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
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 | 128 | 0.67 | 0.89 | 25 | 33Z |
| 2 | 121 | 0.66 | 0.89 | 22 | 33Z |
| 3 | 137 | 0.66 | 0.88 | 23 | 33Z |
| 4 | 294 | 0.55 | 0.76 | 35 | empty |
| 5 | 103 | 0.41 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 466 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 220 Ų buried · 1 hydrogen bond · 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 2PJA · PDBe 2PJA · UniProt P09955
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