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 9OVF | pdb_00009ovf

Rubredoxin covalently linked to benzo-18-crown-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.212 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9OVF

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Site-selective Au(III)-mediated metalloenzyme conjugations.

Adhami, N., Rebelo, M.J.P., Teptarakulkarn, P.H., Ando, S.H., Olivares, E.J., Louis-Goff, T., Munoz, A.J., Raviprolu, V.T., Sawaya, M.R., Han, D., Vaca, I.P., Vlahakis, N.W., Qu, S., Kerr, T.A., Coutinho, R.J., Loo, R.R.O., Loo, J.A., Shafaat, H.S., Rodriguez, J.A., Spokoyny, A.M.

(2026) Chem 

  • DOI: https://doi.org/10.1016/j.chempr.2026.103241
  • Primary Citation Related Structures: 
    9OVF

  • PubMed Abstract: 

    Herein, we introduce an operationally simple approach for the direct covalent modification of metalloenzymes via Au(III)-mediated S -arylation chemistry. Using a model class of rubredoxin metalloenzymes containing Fe or Ni tetrathiolate active site, we demonstrate site-selective installation of diverse abiotic functional groups by targeting a single solvent-exposed cysteine residue distal to the metal center. The bioconjugation proceeds under mild aqueous conditions, rapidly, and in quantitative yields, while preserving the structural and functional integrity of the enzyme. Detailed structural studies, including the first reported X-ray crystal structure of a cysteine-arylated metalloprotein, illuminate a clear preference for regioselective arylation at solvent-exposed cysteine residues, offering a blueprint for predictable and programmable bioconjugation in complex biomolecules. Furthermore, the arylation operates on multiple classes of metalloenzymes including zinc fingers and [3Fe-4S] cluster ferredoxin. This work demonstrates a unique power of "backgroundless" Au(III) arylation chemistry, rendering site-selective bioconjugation of some of the most delicate biomolecules.


  • Organizational Affiliation: 
    • Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, California, 90095, United States.

Macromolecule Content 

  • Total Structure Weight: 60.2 kDa 
  • Atom Count: 4,216 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 450 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rubredoxin-1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
45Desulfovibrio desulfuricans ATCC 27774Mutation(s): 0 
Gene Names: rd1, Ddes_2011
UniProt
Find proteins for P04170 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore P04170 
Go to UniProtKB:  P04170
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04170
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P

Query on 15P



Download:Ideal Coordinates CCD File
QA [auth E],
W [auth B]
POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
A1CET
(Subject of Investigation/LOI)

Query on A1CET



Download:Ideal Coordinates CCD File
BA [auth C]
CB [auth F]
IC [auth J]
JA [auth D]
L [auth A]
BA [auth C],
CB [auth F],
IC [auth J],
JA [auth D],
L [auth A],
LB [auth G],
SA [auth E],
SB [auth H],
U [auth B],
ZB [auth I]
2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol
C16 H24 O6 S
BPELBPJWXAPBFN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AB [auth F]
AC [auth I]
CA [auth C]
DB [auth F]
EA [auth C]
AB [auth F],
AC [auth I],
CA [auth C],
DB [auth F],
EA [auth C],
GC [auth J],
JB [auth G],
JC [auth J],
KA [auth D],
M [auth A],
MA [auth D],
MB [auth G],
N [auth A],
TA [auth E],
TB [auth H],
V [auth B],
VA [auth E],
XB [auth I]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE

Query on FE



Download:Ideal Coordinates CCD File
AA [auth C]
BB [auth F]
HC [auth J]
IA [auth D]
K [auth A]
AA [auth C],
BB [auth F],
HC [auth J],
IA [auth D],
K [auth A],
KB [auth G],
RA [auth E],
RB [auth H],
T [auth B],
YB [auth I]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BC [auth I]
CC [auth I]
DA [auth C]
DC [auth I]
EB [auth F]
BC [auth I],
CC [auth I],
DA [auth C],
DC [auth I],
EB [auth F],
EC [auth I],
FA [auth C],
FB [auth F],
FC [auth J],
GA [auth C],
GB [auth F],
HA [auth C],
HB [auth F],
IB [auth G],
KC [auth J],
LA [auth D],
NA [auth D],
NB [auth G],
O [auth A],
OA [auth D],
OB [auth G],
P [auth A],
PA [auth D],
PB [auth G],
Q [auth A],
QB [auth H],
R [auth A],
S [auth A],
UA [auth E],
UB [auth H],
VB [auth H],
WA [auth E],
WB [auth I],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth B],
ZA [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.212 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 89.15β = 90
c = 94.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM124746-08

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-10-28
    Changes: Database references