9CKT: Papain

X-ray diffraction structure of papain co-crystallized with E-64. Determined by X-ray diffraction at 1.5 Å resolution. Released 4 Jun 2025.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Carica papaya
Chains: 1
Atoms: 2,117
Mol. weight: 23.84 kDa
Ligands: E64, MOH
Released: 4 Jun 2025

Explore 9CKT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CKT contains 8 α-helices and 17 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	14-16	3
β-strand	18	1	2
β-strand	23	1	3
α-helix	25-42	18
β-strand	48	1	4
α-helix	50-56	7
β-strand	64	1	3
α-helix	68-77	10
β-strand	80	1	5
β-strand	82	1	4
β-strand	105	1	5
β-strand	109-112	4	1
α-helix	113-114	2
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

>9CKT_1 Papain (chains A)
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRS
YGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGA
LLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTG
WGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN

Ligands and cofactors

ID	Name	Formula	Copies
E64	N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine	C15 H30 N5 O5	1
MOH	Methanol	C H4 O	1

Primary citation

Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors. Liu, M., Zang, X., Vlahakis, N.W. et al. Nat Chem Biol (2025) 21:1783-1793. DOI 10.1038/s41589-025-01907-2 · 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…
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
1CVZ 1.7 Å, Crystal structure analysis of papain with CLIK148(CATHEPSIN L specific inhibitor)

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