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- PDB-1kpf: PKCI-SUBSTRATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 1kpf
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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity ...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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / cytoskeleton / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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
ADENOSINE MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.5 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: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0662
Polymers13,7191
Non-polymers3471
Water3,135174
1
A: PROTEIN KINASE C INTERACTING PROTEIN
hetero molecules

A: PROTEIN KINASE C INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1324
Polymers27,4382
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5010 Å2
ΔGint-34 kcal/mol
Surface area9620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.150, 40.150, 143.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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.: 1
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer detailsTHE PRODUCT ANALOG (AMP) WAS COCRYSTALLIZED WITH THE PROTEIN. THE AMP STRUCTURE REPORTED HERE ...THE PRODUCT ANALOG (AMP) WAS COCRYSTALLIZED WITH THE PROTEIN. THE AMP STRUCTURE REPORTED HERE REPRESENTS A PRODUCT 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growpH: 6.5 / Details: COCRYSTALLIZED WITH AMP 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 / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 36893 / % possible obs: 84.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.062
Reflection shellHighest resolution: 1.4 Å / Rsym value: 0.259
Reflection
*PLUS
Num. measured all: 158000

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.24 -5 %
Rwork0.209 --
obs0.209 32145 89.5 %
Displacement parametersBiso mean: 12.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 23 174 1063
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_deg1.906
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.599
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
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.801
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.599

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