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- PDB-9hdv: Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in ... -

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Basic information

Entry
Database: PDB / ID: 9hdv
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with a new inhibitor 1-(beta-D-ribofuranosyl) cyanuric acid-5'-monophosphate (YMP)
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Uridine 5'-monophosphate synthase Pyrimidine metabolism Homo sapiens
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PROLINE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKirck, L.L. / Santagostino, E. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2025
Title: Expected and Unexpected "Guests" at the Active Site of Human Orotidine 5'-Monophosphate Decarboxylase.
Authors: Kirck, L.L. / Santagostino, E. / Brandhoff, L. / Simeth, N.A. / Tittmann, K.
History
DepositionNov 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6603
Polymers28,2041
Non-polymers4562
Water3,981221
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3206
Polymers56,4072
Non-polymers9134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3790 Å2
ΔGint-25 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.510, 116.330, 61.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-694-

HOH

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Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase / Orotidine-5'-monophosphate decarboxylase


Mass: 28203.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-A1IT4 / 1-(beta-D-Ribofuranosyl)cyanuric acid-5'-monophosphate / [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[2,4,6-tris(oxidanylidene)-1,3,5-triazinan-1-yl]oxolan-2-yl]methyl dihydrogen phosphate / ((2R,3S,4R,5R)-3,4-dihydroxy-5-(2,4,6-trioxo-1,3,5-triazinan-1-yl)tetrahydrofuran-2-yl)methyl dihydrogen phosphate


Mass: 341.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N3O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 7.0, 1.7 - 1.9 M Ammonium sulfate, 10 mM Glutathion pH 8.0, 5% (w/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 22, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.5→42.41 Å / Num. obs: 45109 / % possible obs: 97.65 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rrim(I) all: 0.1119 / Net I/σ(I): 15.03
Reflection shellResolution: 1.5→1.554 Å / Mean I/σ(I) obs: 2.06 / Num. unique obs: 4477 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.41 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2204 5 %
Rwork0.1922 --
obs0.1934 44124 97.66 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 30 221 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012278
X-RAY DIFFRACTIONf_angle_d1.1653109
X-RAY DIFFRACTIONf_dihedral_angle_d14.707870
X-RAY DIFFRACTIONf_chiral_restr0.238348
X-RAY DIFFRACTIONf_plane_restr0.009409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.34181400.33682659X-RAY DIFFRACTION100
1.53-1.570.2971380.3172622X-RAY DIFFRACTION100
1.57-1.610.3221390.28182640X-RAY DIFFRACTION100
1.61-1.650.27691400.25542653X-RAY DIFFRACTION100
1.65-1.70.27881410.23182669X-RAY DIFFRACTION100
1.7-1.750.24411400.21332650X-RAY DIFFRACTION100
1.75-1.820.23441380.20682635X-RAY DIFFRACTION100
1.82-1.890.25911340.2162543X-RAY DIFFRACTION95
1.89-1.980.36831200.30442295X-RAY DIFFRACTION86
1.98-2.080.18651400.17732664X-RAY DIFFRACTION100
2.08-2.210.23261350.1842577X-RAY DIFFRACTION97
2.21-2.380.29081230.25242369X-RAY DIFFRACTION89
2.38-2.620.20631430.16372701X-RAY DIFFRACTION100
2.62-30.19331430.17862718X-RAY DIFFRACTION100
3-3.780.17781410.16552688X-RAY DIFFRACTION99
3.78-42.410.16671490.15212837X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.0487 Å / Origin y: 15.7119 Å / Origin z: 29.581 Å
111213212223313233
T0.1584 Å2-0.0173 Å2-0.0033 Å2-0.1549 Å20.0103 Å2--0.158 Å2
L0.4444 °20.0138 °2-0.1332 °2-0.925 °20.1672 °2--1.3099 °2
S-0.0086 Å °0.0215 Å °0.0214 Å °-0.021 Å °0.0118 Å °-0.076 Å °-0.0537 Å °0.0749 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

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