4KHQ

Ternary complex of RB69 mutant L415F wit DUMPNPP

> Summary

Summary for 4KHQ

Related4KHU 4KHW 4KHY 4KI4 4KI6 4KHS
DescriptorDNA polymerase (E.C.2.7.7.7), dna
Functional Keywordsnucleotide, transferase-dna complex, transferase/dna
Biological sourceEnterobacteria phage RB69
Total number of polymer chains3
Total molecular weight115268.72
Authors
Clausen, A.R.,Pedersen, L.C. (deposition date: 2013-05-01, release date: 2013-10-09, modification date: 2013-10-30)
Primary citation
Clausen, A.R.,Murray, M.S.,Passer, A.R.,Pedersen, L.C.,Kunkel, T.A.
Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Proc.Natl.Acad.Sci.USA, 110:16802-16807, 2013
PubMed: 24082122
DOI: 10.1073/pnas.1309119110
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.186 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.21420.1%0.8%1.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4khq
no rotation
Molmil generated image of 4khq
rotated about x axis by 90°
Molmil generated image of 4khq
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA polymerasepolymer903104690.01
UniProt (Q38087)
Pfam (PF00136)
Pfam (PF03104)
Enterobacteria phage RB69Gp43
TDNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')polymer185550.71
PDNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')polymer144256.81
CALCIUM IONnon-polymer40.13
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATEnon-polymer467.21
SODIUM IONnon-polymer23.08
waterwater18.0578

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight114497.4
Non-Polymers*Number of molecules12
Total molecular weight771.3
All*Total molecular weight115268.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.186 Å)

Cell axes80.659119.360128.070
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits46.24 - 2.19
the highest resolution shell value2.218 - 2.186
R-factor0.1808
R-work0.17910
the highest resolution shell value0.234
R-free0.21250
the highest resolution shell value0.264
RMSD bond length0.010
RMSD bond angle0.724

Data Collection Statistics

Resolution limits50.00 - 2.19
the highest resolution shell value -
Number of reflections64251
Completeness99.9
Redundancy6
the highest resolution shell value5.2
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.5298

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
A0008408molecular_function3'-5' exonuclease activity
A0003677molecular_functionDNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0046872molecular_functionmetal ion binding
A0000166molecular_functionnucleotide binding
A0039693biological_processviral DNA genome replication
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE CA A 1001
ChainResidue
AASP411
ALEU412
AASP623
ADUP1005

AC22BINDING SITE FOR RESIDUE NA A 1002
ChainResidue
AGLY610
ATHR611

AC35BINDING SITE FOR RESIDUE CA A 1003
ChainResidue
AASP192
AGLU196
AASP860
AHOH1443
AHOH1458

AC46BINDING SITE FOR RESIDUE CA A 1004
ChainResidue
AASN505
AASN507
ALYS531
AHOH1471
AHOH1472
AHOH1554

AC522BINDING SITE FOR RESIDUE DUP A 1005
ChainResidue
AASP411
ALEU412
ATHR413
ASER414
APHE415
ATYR416
AARG482
ALYS560
AASN564
AASP623
ACA1001
ANA1009
AHOH1111
AHOH1124
AHOH1134
AHOH1168
AHOH1323
AHOH1442
AHOH1530
PDC115
TDA3
TDG4

AC67BINDING SITE FOR RESIDUE NA A 1006
ChainResidue
AASP114
AILE115
AGLU116
AHOH1251
AHOH1463
AHOH1464
AHOH1465

AC72BINDING SITE FOR RESIDUE NA A 1007
ChainResidue
AGLU172
AGLU177

AC85BINDING SITE FOR RESIDUE NA A 1008
ChainResidue
AASN232
AHOH1346
AHOH1499
AHOH1539
AHOH1540

AC94BINDING SITE FOR RESIDUE NA A 1009
ChainResidue
AASP411
AASP623
ADUP1005
PDC115

BC15BINDING SITE FOR RESIDUE NA A 1010
ChainResidue
AGLU686
AGLU716
AHOH1134
AHOH1323
AHOH1442

BC26BINDING SITE FOR RESIDUE NA A 1011
ChainResidue
AGLU686
AGLU716
AHOH1134
AHOH1452
AHOH1453
AHOH1545

BC34BINDING SITE FOR RESIDUE NA A 1012
ChainResidue
AGLU660
AASP684
AHOH1178
AHOH1568

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

site_idNumber of ResiduesDetails
DUP_4khq_A_1005182'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE binding site
ChainResidueligand
AASP411-PRO417DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
AARG482DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ALYS486DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ALYS560DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
AASN564DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ATYR567DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ATHR622-ASP623DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
AGLU686DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
TDA3-DG4DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
PDC115DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE

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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
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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