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- PDB-6wk0: Crystal structure of human ribokinase in complex with AMPPCP and ... -

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Basic information

Entry
Database: PDB / ID: 6wk0
TitleCrystal structure of human ribokinase in complex with AMPPCP and ribose
ComponentsRibokinase
KeywordsTRANSFERASE / Enzyme-substrate complex
Function / homology
Function and homology information


ribokinase / ribokinase activity / Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsPark, J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Conformational flexibility of human ribokinase captured in seven crystal structures.
Authors: Akanmori, N.N. / Junop, M.S. / Gupta, R.S. / Park, J.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,46718
Polymers134,9624
Non-polymers2,50514
Water17,619978
1
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7339
Polymers67,4812
Non-polymers1,2537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-82 kcal/mol
Surface area24060 Å2
MethodPISA
2
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7339
Polymers67,4812
Non-polymers1,2537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-80 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.020, 89.350, 144.700
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA14 - 3231 - 310
21LEULEUBB14 - 3231 - 310
12HISHISAA14 - 3301 - 317
22HISHISCC14 - 3301 - 317
13HISHISAA14 - 3281 - 315
23HISHISDD14 - 3281 - 315
14LEULEUBB14 - 3231 - 310
24LEULEUCC14 - 3231 - 310
15LEULEUBB14 - 3231 - 310
25LEULEUDD14 - 3231 - 310
16HISHISCC14 - 3281 - 315
26HISHISDD14 - 3281 - 315

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ribokinase / RK


Mass: 33740.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H477, ribokinase
#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→51.43 Å / Num. obs: 87255 / % possible obs: 98.64 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.059 / Rrim(I) all: 0.113 / Net I/σ(I): 9.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4039 / CC1/2: 0.485 / Rpim(I) all: 0.541 / Rrim(I) all: 1.019 / % possible all: 93.15

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5C41

5c41


Resolution: 2→51.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.447 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23929 4355 5 %RANDOM
Rwork0.19677 ---
obs0.19888 82880 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.676 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.22 Å2
2---0.46 Å20 Å2
3---0.74 Å2
Refinement stepCycle: 1 / Resolution: 2→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9273 0 152 978 10403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139693
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178927
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.66113250
X-RAY DIFFRACTIONr_angle_other_deg1.4381.57720704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90351279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99724.109387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.701151515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4741530
X-RAY DIFFRACTIONr_chiral_restr0.0810.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210894
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021839
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0961.8525095
X-RAY DIFFRACTIONr_mcbond_other1.0951.8525094
X-RAY DIFFRACTIONr_mcangle_it1.6942.7736381
X-RAY DIFFRACTIONr_mcangle_other1.6942.7736382
X-RAY DIFFRACTIONr_scbond_it1.5352.0514598
X-RAY DIFFRACTIONr_scbond_other1.5352.0524599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3043.0316870
X-RAY DIFFRACTIONr_long_range_B_refined6.57324.70210778
X-RAY DIFFRACTIONr_long_range_B_other6.46223.63910472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95050.09
12B95050.09
21A98910.09
22C98910.09
31A96290.09
32D96290.09
41B94440.09
42C94440.09
51B93520.09
52D93520.09
61C93970.1
62D93970.1
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 308 -
Rwork0.284 5822 -
obs--95.22 %
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)
11.8658-0.9354-1.08451.25090.58812.9964-0.064-0.12270.03370.27760.09240.12280.0361-0.0153-0.02830.1167-0.01570.0540.05820.02680.1152-3.2174-3.623874.0366
23.5006-0.35310.36861.4814-0.68442.1843-0.0232-0.00440.01560.1322-0.0678-0.1134-0.10860.20650.09110.0766-0.03370.01310.05220.0110.041511.98642.546563.1353
30.8309-0.3412-0.31222.7638-0.09522.6738-0.1044-0.0560.037-0.09360.13760.0206-0.0155-0.1417-0.03320.1740.0015-0.01740.07250.0050.0035-21.024811.428494.8972
41.0762-0.4380.01223.82530.22362.4938-0.1462-0.17480.03260.35210.1613-0.2079-0.1780.007-0.01510.22570.0921-0.01450.1655-0.01130.0231-17.360712.0756112.7191
51.44320.67541.06743.5492-1.23622.8372-0.08510.05730.0627-0.40660.39370.47880.081-0.4266-0.30860.1232-0.0817-0.07250.25390.14580.161323.063718.683233.3744
62.61260.2908-0.1581.6928-1.39842.7282-0.05950.06-0.0049-0.13160.0646-0.0470.0595-0.0116-0.00510.1025-0.0326-0.0110.06680.01360.028637.853215.351343.7383
70.29610.90260.52942.77841.8223.6184-0.14650.0148-0.0346-0.5730.1405-0.0876-0.20230.32340.0060.7409-0.2367-0.20720.31580.14380.241419.016.522815.0121
81.14430.68240.83942.4945-0.15215.17740.24040.0912-0.27020.0726-0.2096-0.47580.49120.4599-0.03080.4702-0.0212-0.10350.3070.06970.190410.8629-5.56712.9952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 172
2X-RAY DIFFRACTION2A173 - 330
3X-RAY DIFFRACTION3B14 - 166
4X-RAY DIFFRACTION4B167 - 324
5X-RAY DIFFRACTION5C14 - 167
6X-RAY DIFFRACTION6C168 - 330
7X-RAY DIFFRACTION7D14 - 50
8X-RAY DIFFRACTION8D51 - 329

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