MolNFT v1 · #48110 · protein
Crystal structure of activated porcine pancreatic carboxypeptidase B [((R)-1-benzyloxycarbonylamino-hexyl)- hydroxy-phosphinoyloxy]-(3-guanidino-phenyl)-acetic acid complex
2PJ5: “Crystal structure of activated porcine pancreatic carboxypeptidase B [((R)-1-benzyloxycarbonylamino-hexyl)…”. X-ray diffraction, 2 ligands (11B, ZN), 5 pockets (best druggability 0.68). MolNFT v1 #48110 on GenesisL1: 3D structure…
- PDB
- 2PJ5
- 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
- 11B, ZN
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxypeptidase B (EC 3.4.17.2) | protein | 304 | 38% helix, 17% strand | P09955 |
| C | Carboxypeptidase B (EC 3.4.17.2) | protein | 305 | 38% helix, 17% strand | P09955 |
Ligands and binding sites
- 11B · (5R,6S,8S)-8-(3-{[amino(imino)methyl]amino}phenyl)-6-hydroxy-3-oxo-5-pentyl-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
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 | 100 | 0.68 | 0.92 | 24 | 11B |
| 2 | 112 | 0.65 | 0.89 | 24 | 11B |
| 3 | 125 | 0.65 | 0.88 | 27 | 11B |
| 4 | 323 | 0.55 | 0.75 | 33 | empty |
| 5 | 111 | 0.40 | 0.76 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 452 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 193 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 2PJ5 · PDBe 2PJ5 · UniProt P09955
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