1CVZ: Papain

Crystal structure analysis of papain with CLIK148(CATHEPSIN L specific inhibitor). Determined by X-ray diffraction at 1.7 Å resolution. Released 30 Aug 2000.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Carica papaya
Chains: 1
Atoms: 1,814
Mol. weight: 23.86 kDa
Ligands: C48
Released: 30 Aug 2000

Explore 1CVZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1CVZ contains 8 α-helices and 15 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	14-16	3
β-strand	18	1	2
α-helix	25-42	18
β-strand	48	1	3
α-helix	50-56	7
α-helix	62-64	3
α-helix	68-77	10
β-strand	80	1	4
β-strand	82	1	3
β-strand	105	1	4
β-strand	109-112	4	1
α-helix	118-127	10
β-strand	130-134	5	1
α-helix	139-142	4
β-strand	148-149	2	1
β-strand	159-167	9	1
β-strand	170-174	5	1
β-strand	177	1	2
β-strand	183	1	1
β-strand	186-190	5	1
α-helix	199-201	3
β-strand	207-210	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Papain	A	protein	212	Carica papaya	P00784 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1CVZ_1 PAPAIN (chains A)
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRS
YGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGA
LLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTG
WGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN

Ligands and cofactors

ID	Name	Formula	Copies
C48	N1-(1-dimethylcarbamoyl-2-phenyl-ethyl)-2-oxo-N4-(2-pyridin-2-yl-ethyl)-succina…	C22 H26 N4 O4	1

Primary citation

Inhibition mechanism of cathepsin L-specific inhibitors based on the crystal structure of papain-CLIK148 complex. Tsuge, H., Nishimura, T., Tada, Y. et al. Biochem Biophys Res Commun (1999) 266:411-416. DOI 10.1006/bbrc.1999.1830 · PubMed

Other PDB entries of the same protein (UniProt P00784 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CKW 1.4 Å, X-ray diffraction structure of papain co-crystallized with E-64D
9CKY 1.4 Å, X-ray diffraction structure of papain co-crystallized with novel biosynthetic inhibitor…
2CIO 1.5 Å, The high resolution x-ray structure of papain complexed with fragments of the…
9CKT 1.5 Å, X-ray diffraction structure of papain co-crystallized with E-64
9EG7 1.5 Å, X-ray diffraction structure of papain co-crystallized with E64-C
9NB2 1.5 Å, X-ray diffraction structure of papain soaked with E-64
1KHQ 1.6 Å, Orthorhombic form of papain/zlfg-dam covalent complex
1PPN 1.6 Å, Structure of monoclinic papain at 1.60 Å resolution
9CLH 1.6 Å, X-ray diffraction structure of the apo form of papain
9NAT 1.6 Å, X-ray diffraction structure of papain co-crystallized with leupeptin
6TCX 1.65 Å, Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis
9PAP 1.65 Å, Structure of papain refined at 1.65 Å resolution

Browse structure collections

About this viewer

MolViewer shows 1CVZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.