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- PDB-2a2c: x-ray structure of human N-acetyl galactosamine kinase complexed ... -

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Basic information

Entry
Database: PDB / ID: 2a2c
Titlex-ray structure of human N-acetyl galactosamine kinase complexed with Mg-ADP and N-acetyl galactosamine 1-phosphate
ComponentsN-acetylgalactosamine kinase
KeywordsTRANSFERASE / kinase / galactokinase
Function / homology
Function and homology information


N-acetylgalactosamine kinase / N-acetylgalactosamine kinase activity / galactokinase activity / galactose metabolic process / carbohydrate metabolic process / ATP binding / cytosol
Similarity search - Function
de novo design (two linked rop proteins) - #340 / Alpha-Beta Plaits - #3170 / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. ...de novo design (two linked rop proteins) - #340 / Alpha-Beta Plaits - #3170 / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / de novo design (two linked rop proteins) / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-NG1 / N-acetylgalactosamine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The molecular architecture of human N-acetylgalactosamine kinase.
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2019Group: Database references / Structure summary / Category: struct_keywords / struct_ref_seq_dif / Item: _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylgalactosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6006
Polymers52,7891
Non-polymers8115
Water8,233457
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.800, 123.800, 60.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein N-acetylgalactosamine kinase / GalNAc kinase / Galactokinase 2


Mass: 52788.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALK2, GK2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q01415, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Sugar ChemComp-NG1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactopyranose / N-ACETYL-ALPHA-D-GALACTOSAMINE 1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-galactosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactose / 2-acetamido-2-deoxy-1-O-phosphono-D-galactose / 2-acetamido-2-deoxy-1-O-phosphono-galactose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Galp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 461 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG-3400, MES, NaCl, Mg-ATP, N-acetyl galactosamine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926, 0.97940, 0.96411
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.97941
30.964111
ReflectionResolution: 1.65→50 Å / Num. all: 59826 / Num. obs: 59826 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rsym value: 0.054 / Net I/σ(I): 46.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4607 / Rsym value: 0.174 / % possible all: 72.7

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Processing

Software
NameVersionClassification
dSTARTREKdata collection
HKL-2000data reduction
SOLVEphasing
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 5980 -random
Rwork0.167 ---
all0.168 59826 --
obs0.168 59826 94.3 %-
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 49 457 3976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.37

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