5J95

MAP4K4 in complex with inhibitor

> Summary

Summary for 5J95

Related4ZP5
DescriptorMitogen-activated protein kinase kinase kinase kinase 4 (E.C.2.7.11.1)
Functional Keywordskinase, inhibitor complex, structural based drug design, transferase-transferase inhibitor complex, transferase/transferase inhibitor
Biological sourceHomo sapiens (Human)
Cellular locationCytoplasm  O95819
Total number of polymer chains2
Total molecular weight71859
Authors
Liu, S. (deposition date: 2016-04-08, release date: 2017-04-19)
Primary citation
Liu, S.
MAP4K4 in complex with inhibitor
To Be Published,
Experimental method
X-RAY DIFFRACTION (2.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.27431.7%2.5%4.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5j95
no rotation
Molmil generated image of 5j95
rotated about x axis by 90°
Molmil generated image of 5j95
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5j95
no rotation
Molmil generated image of 5j95
rotated about x axis by 90°
Molmil generated image of 5j95
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5j95.pdb1.gz [99.81 KB])
Coordinate files for Biological unit (5j95.pdb2.gz [103.91 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BMitogen-activated protein kinase kinase kinase kinase 4polymer31235733.12
UniProt (O95819)
Homo sapiens (Human)HPK/GCK-like kinase HGK,MAPK/ERK kinase kinase kinase 4,MEKKK 4,Nck-interacting kinase
1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acidnon-polymer392.91
waterwater18.08

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight71466.1
Non-Polymers*Number of molecules1
Total molecular weight392.9
All*Total molecular weight71859.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.5 Å)

Cell axes80.18092.26096.410
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits66.66 - 2.50
the highest resolution shell value2.600 - 2.500
R-factor0.2172
R-work0.21500
the highest resolution shell value0.247
R-free0.25810
the highest resolution shell value0.294
RMSD bond length0.009
RMSD bond angle1.160

Data Collection Statistics

Resolution limits96.40 - 2.50
the highest resolution shell value -
Number of reflections25413
Rmerge_l_obs0.103
the highest resolution shell value1.137
Completeness100.0
Redundancy5.1
the highest resolution shell value6.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP277

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC112binding site for residue 6HH A 4000
ChainResidue
AVAL31
AGLY32
ATYR36
AVAL39
AALA52
AMET105
AGLU106
ACYS108
AASP115
ALEU160
AVAL170
AASP171

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
6HH_5j95_A_4000211-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid binding site
ChainResidueligand
AVAL30-ASN336HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
ATYR366HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
AVAL396HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
AALA526HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
ALYS546HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
AALA836HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
AMET105-SER1126HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
AASP1156HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
ALEU1606HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
AVAL170-ASP1716HH: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Proton acceptor. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000255|PROSITE- ProRule:PRU10027}.
ChainResidueDetails
AASP152

SWS_FT_FI21ATP. {ECO:0000255|PROSITE- ProRule:PRU00159}.
ChainResidueDetails
ALYS53

SWS_FT_FI31ATP. {ECO:0000255|PROSITE- ProRule:PRU00159}.
ChainResidueDetails
AVAL30-VAL38

SWS_FT_FI41Proton acceptor. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000255|PROSITE- ProRule:PRU10027}.
ChainResidueDetails
BASP152

SWS_FT_FI51ATP. {ECO:0000255|PROSITE- ProRule:PRU00159}.
ChainResidueDetails
BLYS53

SWS_FT_FI61ATP. {ECO:0000255|PROSITE- ProRule:PRU00159}.
ChainResidueDetails
BVAL30-VAL38

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5j95.ent.gz (206.07 KB)
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all (no-compress)pdb5j95.ent (791.73 KB)
header onlypdb5j95.ent.gz (6.95 KB)
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PDBx/mmCIF5j95.cif.gz (248.78 KB)
PDBMLall5j95.xml.gz (333.58 KB)
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no-atom5j95-noatom.xml.gz (23.26 KB)
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ext-atom5j95-extatom.xml.gz (107.31 KB)
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PDBMLplusall5j95-plus.xml.gz (335.34 KB)
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no-atom5j95-plus-noatom.xml.gz (25.02 KB)
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add only5j95-add.xml.gz (1.76 KB)
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RDF5j95.rdf.gz (51.94 KB)
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Structure factorsr5j95sf.ent.gz (709.21 KB)
Biological unit (PDB format)5j95.pdb1.gz (99.81 KB) (A)
*author and software defined assembly, 1 molecule(s) (monomeric)
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5j95.pdb2.gz (103.91 KB) (B)
*author and software defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF5j95​_validation.pdf.gz (284.6 KB)
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PDF-full5j95​_full​_validation.pdf.gz (289.3 KB)
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XML5j95​_validation.xml.gz (20.85 KB)
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PNG5j95​_multipercentile​_validation.png.gz (163.15 KB)
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SVG5j95​_multipercentile​_validation.svg.gz (946 B)
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Sequence (fasta)5j95​_seq.txt
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