6H8T | pdb_00006h8t

Crystal structure of Papain modify by achiral Ru(II)complex

PDB DOI: https://doi.org/10.2210/pdb6H8T/pdb
Entry: 6H8T supersedes: 4KP9

Classification: METAL BINDING PROTEIN
Organism(s): Carica papaya
Expression System: Carica papaya
Mutation(s): No

Deposited: 2018-08-03 Released: 2018-09-12
Deposition Author(s): Cherrier, M.V., Amara, P., Talbi, B., Salmin, M., Fontecilla-Camps, J.C.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4KP9

Literature

Crystallographic evidence for unexpected selective tyrosine hydroxylations in an aerated achiral Ru-papain conjugate.

Cherrier, M.V., Amara, P., Talbi, B., Salmain, M., Fontecilla-Camps, J.C.

(2018) Metallomics 10: 1452-1459

PubMed: 30175357 Search on PubMed
DOI: https://doi.org/10.1039/c8mt00160j
Primary Citation Related Structures:
6H8T

PubMed Abstract:
The X-ray structure of an aerated achiral Ru-papain conjugate has revealed the hydroxylation of two tyrosine residues found near the ruthenium ion. The most likely mechanism involves a ruthenium-bound superoxide as the reactive species responsible for the first hydroxylation and the resulting high valent Ru(iv)[double bond, length as m-dash]O species for the second one.

Organizational Affiliation

Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France. juan.fontecilla@ibs.fr.

Macromolecule Content

Total Structure Weight: 48.46 kDa
Atom Count: 3,796
Modeled Residue Count: 426
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain	A, B [auth J]	212	Carica papaya	Mutation(s): 0 EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya) Explore P00784 Go to UniProtKB: P00784
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YXX Query on YXX Download:Ideal Coordinates CCD File SDF format, chain H [auth J] MOL2 format, chain H [auth J] mmCIF format, chain H [auth J]	H [auth J]	chloro(1-{5-[di(pyridin-2-yl-kappaN)amino]pentyl}pyrrolidine-2,5-dione)ruthenium C₁₉ H₂₂ Cl N₄ O₂ Ru LYRJXCXFYIQAEL-UHFFFAOYSA-M		Interactions Focus chain H [auth J] Interactions & Density Focus chain H [auth J]
YXZ Query on YXZ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium C₁₅ H₂₀ Cl N₄ Ru IIQHAXSUPAXJMA-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth J] MOL2 format, chain I [auth J] mmCIF format, chain I [auth J]	I [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth J] Interactions & Density Focus chain I [auth J]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth J] SDF format, chain O [auth J] SDF format, chain N [auth J] SDF format, chain M [auth J] SDF format, chain K [auth J] SDF format, chain J SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain P [auth J] MOL2 format, chain O [auth J] MOL2 format, chain N [auth J] MOL2 format, chain M [auth J] MOL2 format, chain K [auth J] MOL2 format, chain J MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain P [auth J] mmCIF format, chain O [auth J] mmCIF format, chain N [auth J] mmCIF format, chain M [auth J] mmCIF format, chain K [auth J] mmCIF format, chain J mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] E [auth A] F [auth A] J K [auth J] C [auth A], E [auth A], F [auth A], J, K [auth J], M [auth J], N [auth J], O [auth J], P [auth J]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J Focus chain K [auth J] Focus chain M [auth J] Focus chain N [auth J] Focus chain O [auth J] Focus chain P [auth J] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J Focus chain K [auth J] Focus chain M [auth J] Focus chain N [auth J] Focus chain O [auth J] Focus chain P [auth J]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth J] MOL2 format, chain L [auth J] mmCIF format, chain L [auth J]	L [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth J] Interactions & Density Focus chain L [auth J]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMX Query on OMX	A, B [auth J]	L-PEPTIDE LINKING	C₉ H₁₁ N O₄		TYR
TXY Query on TXY	A, B [auth J]	L-PEPTIDE LINKING	C₉ H₁₃ N O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.03	α = 90
b = 74.85	β = 90
c = 86.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Fontecilla-Camps, J.C.

This entry supersedes: 4KP9

Funding Organization	Location	Grant Number
French National Research Agency	France	ARTZYME

Revision History (Full details and data files)

Version 1.0: 2018-09-12
Type: Initial release
Version 1.1: 2018-10-24
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary