[English] 日本語
Yorodumi
- PDB-3bmq: Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bmq
TitleStructure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX5)
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / pteridine reductase / ptr1 / trypanosoma brucei / short chain dehydrogenase / inhibitor
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 6-(benzylsulfanyl)pyrimidine-2,4-diamine / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMartini, V.P. / Iulek, J. / Hunter, W.N.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases.
Authors: Tulloch, L.B. / Martini, V.P. / Iulek, J. / Huggan, J.K. / Lee, J.H. / Gibson, C.L. / Smith, T.K. / Suckling, C.J. / Hunter, W.N.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,31719
Polymers122,7114
Non-polymers4,60615
Water24,5181361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.723, 91.162, 82.832
Angle α, β, γ (deg.)90.00, 115.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ADBC

#1: Protein Pteridine reductase


Mass: 30685.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290
#2: Protein Pteridine reductase


Mass: 30669.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290

-
Non-polymers , 6 types, 1376 molecules

#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-AX5 / 6-(benzylsulfanyl)pyrimidine-2,4-diamine


Mass: 232.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N4S
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1361 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2-3M sodium acetate, 10-100mM sodium citrate, pH 4.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→74.625 Å / Num. obs: 94013 / % possible obs: 85.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.795.50.1474.379587144470.14790.6
1.79-1.95.50.1255.176520138390.12591.6
1.9-2.035.30.1114.561320115340.11181.4
2.03-2.195.70.0768.170582123760.07693.7
2.19-2.45.60.0649.34726784340.06469.2
2.4-2.695.70.05311.160279105300.05395.6
2.69-3.15.70.04611.85371594240.04696.6
3.1-3.85.70.04212.72821449910.04260.6
3.8-5.385.50.03814.22836351860.03881
5.38-13.285.20.03813.61702932520.03891.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→74.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.182 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS All of the 17 related structures are expressed from the same DNA construct, which encodes CYS at positions 59 and 168. Crystals harvested ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS All of the 17 related structures are expressed from the same DNA construct, which encodes CYS at positions 59 and 168. Crystals harvested within a couple of days of formation contain CYS at positions 59 and 168. However these two residues appear quite reactive and over time become oxidised to CSX, as determined by the emergence in older crystals of electron density for the OD atom. Sometimes CYS168 reacts with DTT in the crystallisation buffer, covalently linking the two molecules by an S-S bond.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 4704 5 %RANDOM
Rwork0.131 ---
obs0.134 93474 85.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.34 Å2
2--0.99 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7513 0 298 1361 9172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228195
X-RAY DIFFRACTIONr_bond_other_d0.0020.025366
X-RAY DIFFRACTIONr_angle_refined_deg1.7312.00711205
X-RAY DIFFRACTIONr_angle_other_deg1.0643.00213175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93951080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75524.403318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.412151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9481551
X-RAY DIFFRACTIONr_chiral_restr0.1010.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021508
X-RAY DIFFRACTIONr_nbd_refined0.2240.21891
X-RAY DIFFRACTIONr_nbd_other0.2030.26178
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24009
X-RAY DIFFRACTIONr_nbtor_other0.0870.24122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.21082
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.259
X-RAY DIFFRACTIONr_mcbond_it1.64626656
X-RAY DIFFRACTIONr_mcbond_other0.40122089
X-RAY DIFFRACTIONr_mcangle_it1.96438292
X-RAY DIFFRACTIONr_scbond_it3.0854.53452
X-RAY DIFFRACTIONr_scangle_it4.04662869
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 337 -
Rwork0.174 6446 -
all-6783 -
obs--89.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3844-0.02580.08230.432-0.03460.5648-0.01740.0314-0.0028-0.011-0.0063-0.04990.03130.10530.0237-0.03490.01440.0027-0.02610.0028-0.019211.6489-1.67699.2231
20.4319-0.07960.040.3052-0.02920.4629-0.00410.0505-0.0159-0.0266-0.01090.0341-0.0049-0.0440.0149-0.02940.0049-0.0044-0.0273-0.0024-0.0273-17.27656.3893-1.4221
30.57330.0756-0.00450.36050.08510.5456-0.0124-0.10430.02860.05660.0142-0.025-0.00440.0356-0.0018-0.01680.0049-0.008-0.0206-0.0074-0.03121.29238.266437.7392
40.512-0.05490.04680.30430.02460.5549-0.0199-0.0483-0.02540.02840.00540.04790.038-0.10990.0145-0.0308-0.01250.0125-0.0138-0.0038-0.024-27.7408-0.274527.8976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 26822 - 288
2X-RAY DIFFRACTION2BB2 - 26822 - 288
3X-RAY DIFFRACTION3CC2 - 26822 - 288
4X-RAY DIFFRACTION4DD2 - 26822 - 288

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more