Structure of PDB 3ufx Chain E Binding Site BS01

Receptor Information
>3ufx Chain E (length=373) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLHEYQAKEILARYGVPVPPGKVAYTPEEAKRIAEEFGKRVVIKAQVHV
GGRGKAGGVKLADTPQEAYEKAQAILGMNIKGLTVKKVLVAEAVDIAKEY
YAGLILDRAKKRVVLMLSKEGGVDIEEVAAERPEAIHKFWIDPHKGFRPF
EAREMVKRAGLEGNLNKLAQVLVALYRAYEGVDASIAEINPLVVTTDGGI
VAADAKIVLDDNALFRHPDLAELREVEAEHPLEVEASNYGFAYVKLDGNI
GIIGNGAGLVMYTLDLVNRVGGKPANFLDIGGGAKADVVYNALKVVLKDP
DVKGVFINIFGGITRADEVAKGVIRALEEGLLTKPVVMRVAGTAEEEAKK
LLEGKPVYMYPTSIEAAKVTVAM
Ligand information
Ligand IDGDP
InChIInChI=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
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=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 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(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
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain3ufx Chain E Residue 398 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ufx Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		V43 K45 G52 R53 A93 V94 I96 E99 D204
Binding residue
(residue number reindexed from 1)		V43 K45 G52 R53 A93 V94 I96 E99 D204
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y101 E188
Catalytic site (residue number reindexed from 1) Y101 E188
Enzyme Commision number 6.2.1.4: succinate--CoA ligase (GDP-forming).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004775 succinate-CoA ligase (ADP-forming) activity
GO:0004776 succinate-CoA ligase (GDP-forming) activity
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0006104 succinyl-CoA metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0042709 succinate-CoA ligase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ufx, PDBe:3ufx, PDBj:3ufx
PDBsum3ufx
PubMed22751660
UniProtP25126|SUCC_THETH Succinate--CoA ligase [GDP-forming] subunit beta (Gene Name=sucC)

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