1PIP: Papain

Crystal structure of papain-succinyl-gln-val-val-ala-ala-P-nitroanilide complex at 1.7 Å resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors. Determined by X-ray diffraction at 1.7 Å resolution. Released 31 Oct 1993.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Carica papaya
Chains: 2
Atoms: 1,705
Mol. weight: 24.16 kDa
Released: 31 Oct 1993

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

Secondary structure: helices and β-sheets

1PIP contains 7 α-helices and 13 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: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	25-42	18
β-strand	48	1	2
α-helix	50-56	7
α-helix	68-77	10
β-strand	80	1	3
β-strand	82	1	2
β-strand	105	1	3
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	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)
Succinyl-gln-val-val-ala-ala-P-nitroanilide	B	protein	6

Sequence of entity 1 (A), FASTA

>1PIP_1 Papain (chains A)
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRS
YGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGA
LLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTG
WGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN

Sequence of entity 2 (B), FASTA

>1PIP_2 SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE (chains B)
QVVAAX

Primary citation

Crystal structure of papain-succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide complex at 1.7-A resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors. Yamamoto, A., Tomoo, K., Doi, M. et al. Biochemistry (1992) 31:11305-11309. DOI 10.1021/bi00161a007 · 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

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