Structure of PDB 1xjk Chain A Binding Site BS01

Receptor Information
>1xjk Chain A (length=624) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVAR
VVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLG
VKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAV
KEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISV
VKQGSALMGILNINHPDIEEFIDAKKEVLNFFNLSVGFPMDKKEILKLYE
EDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYP
LYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQ
IAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNS
QEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFA
MGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFL
LAYTRFVTKDDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIP
DVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDD
VLNVYLEALRTNVRGITVYRDGSL
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1xjk Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1xjk Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		N90 S91 A133 G161 G162 K202 A210 N320 P321 C322 E324 P490 T491 G492 S493 I494
Binding residue
(residue number reindexed from 1)		N90 S91 A133 G161 G162 K202 A206 N311 P312 C313 E315 P481 T482 G483 S484 I485
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C134 N320 C322 E324 C333 T626 V627
Catalytic site (residue number reindexed from 1) C134 N311 C313 E315 C324 T617 V618
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005524 ATP binding
GO:0031419 cobalamin binding
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1xjk, PDBe:1xjk, PDBj:1xjk
PDBsum1xjk
PubMed15475969
UniProtO33839

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