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Crystal structure of activated porcine pancreatic carboxypeptidase B 2-(3-aminomethyl-phenyl)-3-[((R)-1- benzyloxycarbonylamino-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: 2PJ2
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: 864, ZN
Pockets: 5 · best druggability 0.64

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

864 · (2S)-2-[3-(aminomethyl)phenyl]-3-[(R)-[(1R)-1-{[(benzyloxy)carbonyl]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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.64	0.89	21	864
2	120	0.62	0.87	24	864
3	121	0.62	0.87	24	864
4	331	0.56	0.75	31	empty
5	92	0.39	0.77	21	empty

Interfaces

2 interfaces between chains.

A–B · 449 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 219 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

2PJ2 · 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 2PJ2 · PDBe 2PJ2 · UniProt P09955

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