9PAP

STRUCTURE OF PAPAIN REFINED AT 1.65 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of papain refined at 1.65 A resolution

Kamphuis, I.G.Kalk, K.H.Swarte, M.B.Drenth, J.

(1984) J Mol Biol 179: 233-256

  • DOI: 10.1016/0022-2836(84)90467-4
  • Primary Citation of Related Structures:  
    9PAP

  • PubMed Abstract: 
  • Papain is a sulfhydryl protease from the latex of the papaya fruit. Its molecules consist of one polypeptide chain with 212 amino acid residues. The chain is folded into two domains with the active site in a groove between the domains. We have refined the crystal structure of papain, in which the sulfhydryl group was oxidized, by a restrained least-squares procedure at 1 ...

    Papain is a sulfhydryl protease from the latex of the papaya fruit. Its molecules consist of one polypeptide chain with 212 amino acid residues. The chain is folded into two domains with the active site in a groove between the domains. We have refined the crystal structure of papain, in which the sulfhydryl group was oxidized, by a restrained least-squares procedure at 1.65 A to an R-factor of 16.1%. The estimated accuracy in the atomic co-ordinates is 0.1 A, except for disordered atoms. All phi/psi angles for non-glycine residues are found within the outer limit boundary of a Ramachandran plot and this provides another check on the quality of the model. In the alpha-helical parts of the structure, the C = O bonds are directed more away from the helix axis than in a classical alpha-helix, leading to somewhat longer hydrogen bonds, 2.98 A, compared to 2.89 A. The hydrogen-bonding parameters and conformational angles in the anti-parallel beta-sheet structure show a large diversity. Hydrogen bonds in the core of the sheet are generally shorter than those at the more twisted ends. The average value is 2.91 A. The hydrogen bond distance Ni+3-Oi in turns is relatively long and the geometry is far from linear. Hydrogen bond formation, therefore, is perhaps not an essential prerequisite for turn formation. Although the crystallization medium is 62% (w/w) methanol in water, only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules. The water molecules play an important role in maintaining structural stability. This is specially true for internal water. Twenty-one water molecules are located in contact areas between adjacent papain molecules. It seems as if the enzyme is trapped in a grid of water molecules with only a limited number of direct interactions between the protein molecules. The residues in the active site cleft belong to the most static parts of the structure. In general, disorder in atomic positions increases when going from the interior of the protein molecule to its surface. This behavior was quantified and it was found that the point of minimum disorder is near the molecular centroid.


    Related Citations: 
    • Thiol Proteases. Comparative Studies Based on the High-Resolution Structures of Papain and Actinidin, and on Amino Acid Sequence Information for Cathepsins B and H, and Stem Bromelain
      Kamphuis, I.G., Drenth, J., Baker, E.N.
      (1985) J Mol Biol 182: 317
    • Binding of Chloromethyl Ketone Substrate Analogues to Crystalline Papain
      Drenth, J., Kalk, K.H., Swen, H.M.
      (1976) Biochemistry 15: 3731
    • The Structure of Papain
      Drenth, J., Jansonius, J.N., Koekoek, R., Wolthers, B.G.
      (1971) Adv Protein Chem 25: 79
    • The Structure of the Papain Molecule
      Drenth, J., Jansonius, J.N., Koekoek, R., Sluyterman, L.A.A., Wolthers, B.G.
      (1970) Philos Trans R Soc London,ser B 257: 231
    • Structure of Papain
      Drenth, J., Jansonius, J.N., Koekoek, R., Swen, H.M., Wolthers, B.G.
      (1968) Nature 218: 929

    Organizational Affiliation

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 0600810, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PAPAINA212Carica papayaMutation(s): 0 
EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya)
Explore P00784 
Go to UniProtKB:  P00784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00784
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOH
Query on MOH

Download Ideal Coordinates CCD File 
AA [auth A],
B [auth A],
BA [auth A],
C [auth A],
CA [auth A],
AA [auth A],
B [auth A],
BA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.2α = 90
b = 104.64β = 90
c = 50.88γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1986-10-24
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other