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- PDB-6lig: Crystal structure of human Glutamate oxaloacetate transaminase 1 ... -

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Basic information

Entry
Database: PDB / ID: 6lig
TitleCrystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1) in complex with AH
ComponentsGlutamate oxaloacetate transaminase 1
KeywordsTRANSFERASE / inhibitor
Function / homology
Function and homology information


phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process ...phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / Aspartate and asparagine metabolism / 2-oxoglutarate metabolic process / oxaloacetate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / Gluconeogenesis / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-EE6 / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsYan, S. / Sun, W.G. / Zhang, Y.H.
CitationJournal: To Be Published
Title: Crystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1) in complex with AH
Authors: Shan, Y.
History
DepositionDec 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate oxaloacetate transaminase 1
B: Glutamate oxaloacetate transaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8744
Polymers92,1942
Non-polymers6802
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-23 kcal/mol
Surface area30410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.870, 90.420, 74.050
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamate oxaloacetate transaminase 1 / Aspartate aminotransferase / cytoplasmic / cAspAT / Cysteine aminotransferase / cytoplasmic / ...Aspartate aminotransferase / cytoplasmic / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Transaminase A


Mass: 46097.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P17174, aspartate transaminase, cysteine transaminase
#2: Chemical ChemComp-EE6 / 3-[3-(3-methylbut-2-enyl)-4-oxidanyl-phenyl]-5-[[3-(3-methylbut-2-enyl)-4-oxidanyl-phenyl]methylidene]-4-oxidanyl-furan-2-one


Mass: 432.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.62→64.8553 Å / Num. obs: 25267 / % possible obs: 97.67 % / Redundancy: 2 % / CC1/2: 0.989 / Net I/σ(I): 9.34
Reflection shellResolution: 2.62→2.714 Å / Num. unique obs: 2557 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DND

6dnd


Resolution: 2.62→64.835 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.43
RfactorNum. reflection% reflection
Rfree0.2661 1982 7.85 %
Rwork0.2127 --
obs0.2169 25245 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.46 Å2 / Biso mean: 29.9613 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 2.62→64.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6453 0 48 174 6675
Biso mean--31.92 27.25 -
Num. residues----820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.62-2.68560.32151420.265166998
2.6856-2.75820.35221410.2635166498
2.7582-2.83930.30761360.2623158994
2.8393-2.9310.31751480.2527168299
2.931-3.03570.32851420.2505165699
3.0357-3.15730.33491410.2554168399
3.1573-3.3010.25461460.2425165799
3.301-3.4750.25241440.2163170999
3.475-3.69270.27971410.2023166799
3.6927-3.97780.2281360.1898164097
3.9778-4.3780.26221370.1717161494
4.378-5.01130.21751450.1671169699
5.0113-6.31290.26511430.2094167198
6.3129-64.8350.19561400.1931166695
Refinement TLS params.Method: refined / Origin x: -19.6561 Å / Origin y: 2.458 Å / Origin z: -28.1362 Å
111213212223313233
T0.0119 Å2-0.0045 Å20.0045 Å2-0.0005 Å2-0.0133 Å2--0.0246 Å2
L0.1471 °2-0.0279 °2-0.0063 °2-0.0928 °2-0.0425 °2--0.1453 °2
S-0.0122 Å °0.0367 Å °0.0056 Å °0.0566 Å °-0.0119 Å °-0.0089 Å °0.0569 Å °0.0373 Å °-0.0069 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 412
2X-RAY DIFFRACTION1allA413
3X-RAY DIFFRACTION1allB3 - 412
4X-RAY DIFFRACTION1allB413
5X-RAY DIFFRACTION1allS1 - 174

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