Structure of PDB 3o0o Chain A Binding Site BS02

Receptor Information

>3o0o Chain A (length=612) Species: 2336 (Thermotoga maritima)

MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVAR
VVATAELLNPSKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDL
LWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYAL
ITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGS
RRGALMGILNINHPDIEEFIDAKKVLNFFNLSVGFPMDKKEILKLYEEDG
ELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYP
HRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAV
RFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEA
RDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGM
SNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAY
TRFPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVV
ALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTN
VRGITVYRDGSL

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: 3o0o Chain A Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o0o Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): S91 A133 C134 G161 G162 N320 C322 P490 T491 G492 S493 I494
• Binding residue (residue number reindexed from 1): S86 A128 C129 G156 G157 N308 C310 P478 T479 G480 S481 I482
• 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): C129 N308 C310 E312 C321 T605 V606
• 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:3o0o, PDBe:3o0o, PDBj:3o0o
• PDBsum: 3o0o
• PubMed: 20672854
• UniProt: O33839