Structure of PDB 1xjg Chain B Binding Site BS03

Receptor Information

>1xjg Chain B (length=610) Species: 2336 (Thermotoga maritima)

MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVAR
VVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLG
VKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAV
KEYALITKVGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVV
KQALMGILNINHPDIEEFIDAKKVLNFFNLSVGFPMDKKEILKLYEEDGE
LELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPH
RKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVR
FLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEAR
DFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMS
NYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYT
RFLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVAL
DIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVR
GITVYRDGSL

Ligand information

• Ligand ID: DTP
• InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
• InChIKey: SUYVUBYJARFZHO-RRKCRQDMSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H16 N5 O12 P3
• Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL335538
• DrugBank: DB03222
• ZINC: ZINC000008215662
• PDB chain: 1xjg Chain B Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1xjg Structural Mechanism of Allosteric Substrate Specificity Regulation in a Ribonucleotide Reductase
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): D141 S142 I143 R171 V177 A178 A184 S185
• Binding residue (residue number reindexed from 1): D141 S142 I143 R170 V176 A177 A183 S184
• Annotation score: 1

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 T603 V604
• 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

External links

• PDB: RCSB:1xjg, PDBe:1xjg, PDBj:1xjg
• PDBsum: 1xjg
• PubMed: 15475969
• UniProt: O33839