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- PDB-1av5: PKCI-SUBSTRATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 1av5
TitlePKCI-SUBSTRATE ANALOG
ComponentsPROTEIN KINASE C INTERACTING PROTEIN
KeywordsPROTEIN KINASE INHIBITOR / PKCI-1 / HIT PROTEIN FAMILY / HISTIDINE TRIAD PROTEIN FAMILY / NUCLEOTIDYL HYDROLASE / NUCLEOTIDYL TRANSFERASE
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLima, C.D. / Klein, M.G. / Hendrickson, W.A.
Citation
Journal: Science / Year: 1997
Title: Structure-based analysis of catalysis and substrate definition in the HIT protein family.
Authors: Lima, C.D. / Klein, M.G. / Hendrickson, W.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Three-Dimensional Structure of Human Protein Kinase C Interacting Protein 1, a Member of the Hit Family of Proteins
Authors: Lima, C.D. / Klein, M.G. / Weinstein, I.B. / Hendrickson, W.A.
History
DepositionSep 25, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN KINASE C INTERACTING PROTEIN
B: PROTEIN KINASE C INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8633
Polymers27,4382
Non-polymers4251
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-27 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.200, 77.800, 80.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN KINASE C INTERACTING PROTEIN / PKCI-1 / PROTEIN KINASE C INHIBITOR 1 / HINT PROTEIN / HIT PROTEIN


Mass: 13718.772 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPKCI-1 / Plasmid: PHIL-D5 / Gene (production host): HPKCI-1 / Production host: Pichia pastoris (fungus) / References: UniProt: P49773
#2: Chemical ChemComp-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer detailsTHE SUBSTRATE ANALOG (AMPCP) WAS SOAKED INTO THE CRYSTAL AND FOUND TO BIND IN THE ACTIVE SITE OF ...THE SUBSTRATE ANALOG (AMPCP) WAS SOAKED INTO THE CRYSTAL AND FOUND TO BIND IN THE ACTIVE SITE OF CHAIN B. THE ACTIVE SITE OF CHAIN A IS BLOCKED BY A LATTICE CONTACT AND IS NOT AVAILABLE TO THE SUBSTRATE. THE AMPCP STRUCTURE REPORTED HERE REPRESENTS A SUBSTRATE ANALOG FOR PKCI IN THE CHARACTERIZED REACTION WITH ADP AS SUBSTRATE.

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growpH: 6.5 / Details: GROWN FROM PEG8K PH6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: Lima, C.D., (1996) Proc.Nat.Acad.Sci.USA, 93, 5357.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-18 %PEG80001reservoir
2100 mMsodium cacodylate1reservoir
33-6 mg/mlPKCI-11drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 17, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 14358 / % possible obs: 71.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Num. obs: 26213 / Num. measured all: 194693

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
Details: REFINED ADENOSINE ALPHA/BETA-METHYLENE DIPHOSPHATE AS ADP.
RfactorNum. reflection% reflection
Rfree0.279 -5 %
Rwork0.229 --
obs0.229 25149 66.9 %
Displacement parametersBiso mean: 31 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 27 0 122 1896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.211
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.55
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.944
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.557
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.944

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