Structure of PDB 7jmk Chain B Binding Site BS01

Receptor Information
>7jmk Chain B (length=379) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLQEYQSKKLMSDNGVKVQRFFVADTANELNAKEIVLKAQILAGGRGLK
GGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRE
TYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKD
SQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEG
QVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIENEAAKYDLKYIGLDG
NIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKESQVYQAFKLLTA
DPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVHEA
QNILTNSGLPITSAVDLEDAAKKAVASVT
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 chain7jmk Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7jmk Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K46 R54 V67 L69 L109 I111 E114 V138
Binding residue
(residue number reindexed from 1)		K39 R47 V53 L55 L95 I97 E100 V124
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y116 E204
Catalytic site (residue number reindexed from 1) Y102 E190
Enzyme Commision number 6.2.1.4: succinate--CoA ligase (GDP-forming).
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004775 succinate-CoA ligase (ADP-forming) activity
GO:0004776 succinate-CoA ligase (GDP-forming) activity
GO:0005515 protein binding
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:0005739 mitochondrion
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:7jmk, PDBe:7jmk, PDBj:7jmk
PDBsum7jmk
PubMed
UniProtP53590|SUCB2_PIG Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (Fragment) (Gene Name=SUCLG2)

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