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Crystal structure of activated porcine pancreatic carboxypeptidase B

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: 1Z5R
Type: protein
Length: 912 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Procarboxypeptidase B
EC: 3.4.17.2
UniProt: P09955
Ligands: ZN
Pockets: 6 · 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	Procarboxypeptidase B (EC 3.4.17.2)	protein	304	38% helix, 17% strand	P09955

Ligands and binding sites

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

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.64	0.84	26	empty
2	156	0.64	0.86	24	empty
3	227	0.64	0.83	31	ZN
4	210	0.49	0.75	27	empty
5	90	0.41	0.78	20	empty

Interfaces

2 interfaces between chains.

A–B · 459 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 228 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

1Z5R · 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 1Z5R · PDBe 1Z5R · UniProt P09955

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