9NBN: Papain

Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with a mixture of E-64, E-64C, and E-64D. Determined by X-ray diffraction at 1.8 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Carica papaya
Chains: 1
Atoms: 1,777
Mol. weight: 23.7 kDa
Ligands: A1BWS
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

9NBN contains 9 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: 9 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
α-helix	98-100	3
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

>9NBN_1 Papain (chains A)
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRS
YGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGA
LLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTG
WGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN

Ligands and cofactors

ID	Name	Formula	Copies
A1BWS	(3S)-4-{[(2S)-1-amino-4-methyl-1-oxopentan-2-yl]amino}-3-hydroxy-4-oxobutanoic…	C10 H18 N2 O5	1

Primary citation

Combining MicroED and native mass spectrometry for structural discovery of enzyme-biosynthetic inhibitor complexes. Vlahakis, N.W., Flowers, C.W., Liu, M. et al. bioRxiv (2025). DOI 10.1101/2025.02.20.638743 · 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

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