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- PDB-5c40: Crystal structure of human ribokinase in complex with AMPPCP in P... -

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Basic information

Entry
Database: PDB / ID: 5c40
TitleCrystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup
ComponentsRibokinase
KeywordsTRANSFERASE
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 / PHOSPHATE ION / Ribokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPark, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.
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
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references / Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,86911
Polymers70,4822
Non-polymers1,3879
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-20 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.790, 72.420, 92.750
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 15 - 325 / Label seq-ID: 15 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribokinase


Mass: 35241.008 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium HEPES, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.5→27.12 Å / Num. obs: 96118 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.297 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7


Resolution: 1.5→27.12 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.207 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18132 4826 5 %RANDOM
Rwork0.12659 ---
obs0.12931 91278 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.12 Å2
2---0.25 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 81 711 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194997
X-RAY DIFFRACTIONr_bond_other_d0.0120.024734
X-RAY DIFFRACTIONr_angle_refined_deg2.3241.996848
X-RAY DIFFRACTIONr_angle_other_deg1.856310915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77725.652184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93115808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5271514
X-RAY DIFFRACTIONr_chiral_restr0.1540.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025747
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021060
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_it2.5571.7012611
X-RAY DIFFRACTIONr_mcbond_other2.5641.6992610
X-RAY DIFFRACTIONr_mcangle_it2.8942.553296
X-RAY DIFFRACTIONr_mcangle_other2.9042.5513297
X-RAY DIFFRACTIONr_scbond_it3.9652.1092386
X-RAY DIFFRACTIONr_scbond_other3.9382.1012375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.183.0093535
X-RAY DIFFRACTIONr_long_range_B_refined4.44215.9916092
X-RAY DIFFRACTIONr_long_range_B_other3.94314.7725650
X-RAY DIFFRACTIONr_rigid_bond_restr6.61839731
X-RAY DIFFRACTIONr_sphericity_free27.0635171
X-RAY DIFFRACTIONr_sphericity_bonded10.744510189
Refine LS restraints NCS

Ens-ID: 1 / Number: 36368 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 352 -
Rwork0.234 6666 -
obs--98.43 %

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