Structure of PDB 3ir6 Chain A Binding Site BS02

Receptor Information

>3ir6 Chain A (length=1233) Species: 83333 (Escherichia coli K-12)

SKFLDRFRQKGETFADGHGQLLNTNRDWEDGYRQRWQHDKIVRSTSCSWK
IYVKNGLVTWETQQTDYPRTRPDLPNHEPRGCPRGASYSWYLYSANRLKY
PMMRKRLMKMWREAKALHSDPVEAWASIIEDADKAKSFKQARGRGGFVRS
SWQEVNELIAASNVYTIKNYGPDRVAGFSPIPAMSMVSYASGARYLSLIG
GTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGSNVPQTR
TPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMG
HVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLEERDGYYAAGRMLRAADL
VDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKWNLEQRDGKTG
EETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRL
QLADGSTALVTTVYDLTLANYGLERGLNDVNCATSYDDVKAYTPAWAEQI
TGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRGLINM
LIFCGCVGQSGGGWAHYVGEKLRPQTGWQPLAFALDWQRPARHMNSTSYF
YNHSSQWRYETVTAEELLSPMADKSRYTGHLIDFNVRAERMGWLPSAPQL
GTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFI
WRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGL
EGKLDLVVTLDFRLSSTCLYSDIILPTATWYEKDDMNTSDMHPFIHPLSA
AVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELA
QPLDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGN
GGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAAEMILTLAPE
TNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPT
WSGLEDEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVY
RPPIDTRSVKEVIGQKSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG
RGGPVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGMTMM
YHAQERIVNLPGSEITQQRGGIHNSVTRITPKPTHMIGGYAHLAYGFNYY
GTVGSNRDEFVVVRKMKNIDWLDGEGNDQVQES

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: 3ir6 Chain A Residue 1248

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ir6 Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G253 N255 T259 V280 T281 P282 D283 D302 G541 A542 G543 L544 W547 P1091 H1092
• Binding residue (residue number reindexed from 1): G243 N245 T249 V270 T271 P272 D273 D292 G531 A532 G533 L534 W537 P1080 H1081
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): R94 P190 W219 Y220 P224
• Catalytic site (residue number reindexed from 1): R84 P180 W209 Y210 P214
• Enzyme Commision number: 1.7.5.1: nitrate reductase (quinone).

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008940 nitrate reductase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0160182 nitrate reductase (quinone) activity

Biological Process

• GO:0009061 anaerobic respiration
• GO:0019645 anaerobic electron transport chain
• GO:0042126 nitrate metabolic process
• GO:0042128 nitrate assimilation
• GO:0045333 cellular respiration

Cellular Component

• GO:0005886 plasma membrane
• GO:0009325 nitrate reductase complex
• GO:0016020 membrane
• GO:0044799 NarGHI complex
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:3ir6, PDBe:3ir6, PDBj:3ir6
• PDBsum: 3ir6
• PubMed: 20053990
• UniProt: P09152|NARG_ECOLI Respiratory nitrate reductase 1 alpha chain (Gene Name=narG)