Structure of PDB 2ywc Chain D Binding Site BS01

Receptor Information
>2ywc Chain D (length=467) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVLVLDFGSQYTRLIARRLRELRAFSLILPGDAPLEEVLKHRPQALILSG
GPRSVFDPDAPRPDPRLFSSGLPLLGICYGMQLLAQELGGRVERAGRAEY
GKALLTRHEGPLFRGLEGEVQVWMSHQDAVTAPPPGWRVVAETEENPVAA
IASPDGRAYGVQFHPEVAHTPKGMQILENFLELAGVKRDWTPEHVLEELL
REVRERAGKDRVLLAVSGGVDSSTLALLLAKAGVDHLAVFVDHGLLRLGE
REEVEGALRALGVNLLVVDAKERFLKALKGVEDPEEKRKIIGREFVAAFS
QVARERGPFRFLAQGTLYPDVIFELLEPFRLLFKDEVRELALLLGLPDTL
RLRHPFPGPGLAVRVLGEVTEERLEILRRADDIFTSLLREWGLYEKVAQA
LAVLTPVRGYVLALRAVTTEDFMTADWARLPLEFLDEAARRITRRVPEIG
RVVYDLTSKPPATIEWE
Ligand information
Ligand IDXMP
InChIInChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/p+1/t3-,5-,6-,9-/m1/s1
InChIKeyDCTLYFZHFGENCW-UUOKFMHZSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)NC(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23
OpenEye OEToolkits 1.5.0c1[nH+]c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)NC(=O)NC2=O
ACDLabs 10.04O=C3Nc1c([nH+]cn1C2OC(C(O)C2O)COP(=O)(O)O)C(=O)N3
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23
FormulaC10 H14 N4 O9 P
NameXANTHOSINE-5'-MONOPHOSPHATE;
5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE
ChEMBL
DrugBank
ZINC
PDB chain2ywc Chain D Residue 704 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ywc Crystal structure of GMP synthetase from Thermus thermophilus
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R288 P382 G383 P384 Q424 F458 K495 T499 I500 E501
Binding residue
(residue number reindexed from 1)		R288 P357 G358 P359 Q399 F422 K459 T463 I464 E465
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) G51 R53 C78 Y79 H164 E166 D221 K359
Catalytic site (residue number reindexed from 1) G51 R53 C78 Y79 H164 E166 D221 K334
Enzyme Commision number 6.3.5.2: GMP synthase (glutamine-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003921 GMP synthase activity
GO:0003922 GMP synthase (glutamine-hydrolyzing) activity
GO:0005524 ATP binding
GO:0016874 ligase activity
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006177 GMP biosynthetic process
GO:0006541 glutamine metabolic process
GO:0044281 small molecule metabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ywc, PDBe:2ywc, PDBj:2ywc
PDBsum2ywc
PubMed
UniProtQ5SI28|GUAA_THET8 GMP synthase [glutamine-hydrolyzing] (Gene Name=guaA)

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