Structure of PDB 1xje Chain B Binding Site BS02

Receptor Information

>1xje Chain B (length=618) Species: 2336 (Thermotoga maritima)

MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVAR
VVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLG
VKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAV
KEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISV
VKQGSRRRGALMGILNINHPDIEEFIDAKKVLNFFNLSVGFPMDKKEILK
LYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNK
YYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQE
LVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIP
YNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFV
PFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEP
NFLLAYTRFPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKI
KKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYL
EALRTNVRGITVYRDGSL

Ligand information

• Ligand ID: GDP
• InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 1xje Chain B Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1xje Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): N90 S91 A133 G161 R207 R208 A210 N320 C322 E324 P490 T491 G492 S493 I494
• Binding residue (residue number reindexed from 1): N90 S91 A133 G161 R207 R208 A210 N314 C316 E318 P484 T485 G486 S487 I488
• 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 N314 C316 E318 C327 T611 V612
• 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:1xje, PDBe:1xje, PDBj:1xje
• PDBsum: 1xje
• PubMed: 15475969
• UniProt: O33839