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Crystal structure of activated porcine pancreatic carboxypeptidase B (S)-2-(3-aminomethyl-phenyl)-3-{hydroxy- [(R)-2-methyl-1-(3-phenyl-propane-1-sulfonylamino)-propyl]- phosphinoyl}-propionic acid {zk 528} 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: 2PIY
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: 528, ZN
Pockets: 5 · best druggability 0.65

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

528 · (2S)-2-[3-(aminomethyl)phenyl]-3-{(R)-hydroxy[(1r)-2-methyl-1-{[(3-phenylpropyl)sulfonyl]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

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.65	0.89	22	528
2	136	0.62	0.86	25	528
3	133	0.61	0.86	24	528
4	326	0.56	0.76	35	empty
5	99	0.38	0.75	24	empty

Interfaces

2 interfaces between chains.

A–B · 457 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 234 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

2PIY · CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B… · the same entry in another collection · chain A against A, TM-score 1.00
P09955 · AlphaFold monomer V2.0 prediction for carboxypeptidase B (P09955) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 2PIY · PDBe 2PIY · UniProt P09955

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