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- PDB-9dqa: Crystal structure of bovine RPE65 in complex with EYE-002 -

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Basic information

Entry
Database: PDB / ID: 9dqa
TitleCrystal structure of bovine RPE65 in complex with EYE-002
ComponentsRetinoid isomerohydrolase
KeywordsISOMERASE/INHIBITOR / 7-BLADED BETA PROPELLER / MONOTOPIC MEMBRANE PROTEIN / NON-HEME IRON ENZYME / RETINOID ISOMERASE / INHIBITOR / COMPLEX / HYDROLASE / ISOMERASE / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / detection of light stimulus involved in visual perception / retinal metabolic process ...retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / detection of light stimulus involved in visual perception / retinal metabolic process / phosphatidylcholine binding / cardiolipin binding / retina homeostasis / phosphatidylserine binding / endoplasmic reticulum membrane / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
: / : / PALMITIC ACID / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsKiser, P.D. / Bassetto, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Veterans Affairs (VA, United States)BX004939 United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Rationally Designed, Short-Acting RPE65 Inhibitors for Visual Cycle-Associated Retinopathies.
Authors: Bassetto, M. / Hu, Y. / Li, B. / Chen, X. / Saraswat, V. / Damacio, F. / Smidak, R. / Palczewski, K. / Tochtrop, G.P. / Kiser, P.D.
History
DepositionSep 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoid isomerohydrolase
B: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2368
Polymers122,0802
Non-polymers1,1556
Water17,781987
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-36 kcal/mol
Surface area36600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.810, 175.810, 86.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 533 / Label seq-ID: 3 - 533

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Retinoid isomerohydrolase / All-trans-retinyl-palmitate hydrolase / Lutein isomerase / Meso-zeaxanthin isomerase / Retinal ...All-trans-retinyl-palmitate hydrolase / Lutein isomerase / Meso-zeaxanthin isomerase / Retinal pigment epithelium-specific 65 kDa protein / Retinol isomerase


Mass: 61040.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q28175, retinoid isomerohydrolase, lutein isomerase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1BEO / 3-[(1R)-3-amino-1-hydroxypropyl]phenyl 2-ethylbutanoate


Mass: 265.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 30% PEG 200, 200 mM ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 87750 / % possible obs: 98.8 % / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.22 Å / Rmerge(I) obs: 2.025 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 12591 / CC1/2: 0.298

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→47.906 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.711 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2089 4497 5.125 %
Rwork0.1801 83253 -
all0.182 --
obs-87750 98.77 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.828 Å20.414 Å20 Å2
2--0.828 Å2-0 Å2
3----2.687 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8153 0 76 987 9216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0128660
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168019
X-RAY DIFFRACTIONr_angle_refined_deg0.9141.83511802
X-RAY DIFFRACTIONr_angle_other_deg0.3341.75918550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80651048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.992536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.511101389
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.37310414
X-RAY DIFFRACTIONr_chiral_restr0.0470.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022010
X-RAY DIFFRACTIONr_nbd_refined0.1710.21423
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.27728
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24093
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2955
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.26
X-RAY DIFFRACTIONr_nbd_other0.1620.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.220
X-RAY DIFFRACTIONr_mcbond_it1.94.9884144
X-RAY DIFFRACTIONr_mcbond_other1.8984.9884144
X-RAY DIFFRACTIONr_mcangle_it3.2448.9455199
X-RAY DIFFRACTIONr_mcangle_other3.2458.9465200
X-RAY DIFFRACTIONr_scbond_it2.0865.2534516
X-RAY DIFFRACTIONr_scbond_other2.0865.2534517
X-RAY DIFFRACTIONr_scangle_it3.5819.5216600
X-RAY DIFFRACTIONr_scangle_other3.5819.5226601
X-RAY DIFFRACTIONr_lrange_it6.841130.2859782
X-RAY DIFFRACTIONr_lrange_other6.84130.2939781
X-RAY DIFFRACTIONr_ncsr_local_group_10.0560.0517180
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.055840.0501
12AX-RAY DIFFRACTIONLocal ncs0.055840.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.3823350.35855470.35965520.8180.83389.77410.358
2.154-2.2130.3312780.34357330.34263450.9210.90594.7360.339
2.213-2.2770.3053360.30658600.30662210.9190.91999.59810.295
2.277-2.3470.3063000.27156870.27359870.9250.9441000.252
2.347-2.4240.2692950.25655470.25658420.9430.951000.231
2.424-2.5090.242760.22953550.22956320.9550.96299.98220.202
2.509-2.6030.2322640.2251720.22154360.9620.9661000.191
2.603-2.7090.242680.2149940.21152620.9630.9711000.179
2.709-2.8290.2322860.19847480.250350.9650.97599.98010.169
2.829-2.9670.2332110.18845840.1948120.9660.97899.64670.159
2.967-3.1270.2042310.17943480.18145790.9720.9811000.156
3.127-3.3160.2042360.16741160.16943520.9730.9831000.149
3.316-3.5430.2221780.1638730.16240510.970.9851000.148
3.543-3.8260.192160.15436070.15638230.9760.9861000.145
3.826-4.1880.191590.14533480.14735150.980.98799.77240.14
4.188-4.6780.1531710.12230100.12331870.9860.99199.81170.124
4.678-5.3930.1411630.12426610.12528240.9890.9911000.127
5.393-6.5840.1651100.1522880.15123990.9850.98999.95830.153
6.584-9.2250.1991010.15817580.1618790.9780.98698.93560.166
9.225-47.9060.227830.21710170.21811010.960.96699.90920.241

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