Structure of PDB 1xjg Chain A Binding Site BS01

Receptor Information
>1xjg Chain A (length=615) 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
VKALMGILNINHPDIEEFIDAKKVLNFFNLSVGFPMDKKEILKLYEEDGE
LELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPH
RKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVR
FLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEAR
DFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMS
NYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYT
RFVTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKV
FVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEAL
RTNVRGITVYRDGSL
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain1xjg 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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PDB1xjg Structural Mechanism of Allosteric Substrate Specificity Regulation in a Ribonucleotide Reductase
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N90 S91 A133 N320 P321 C322 E324 P490 T491 S493 I494
Binding residue
(residue number reindexed from 1)		N90 S91 A133 N307 P308 C309 E311 P477 T478 S480 I481
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 N307 C309 E311 C320 T608 V609
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:1xjg, PDBe:1xjg, PDBj:1xjg
PDBsum1xjg
PubMed15475969
UniProtO33839

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