Structure of PDB 1kv3 Chain F Binding Site BS01

Receptor Information
>1kv3 Chain F (length=651) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETNGRDHHTADLCREKLVVRRGQPFWLTLSLTFSVVTGPAPSQEAGTKAR
FPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASGHFI
LLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFQ
DGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVGSGMVNCNDDQGV
LLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACT
VLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHC
WVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLST
KYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDER
EDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMG
SDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLTLEP
FSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLEN
PEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTV
EIPDPVEAGEEVKVRMDLVPLHMGLHKLVVNFESDKLKAVKGFRNVIIGP
A
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 chain1kv3 Chain F Residue 705 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1kv3 Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		F174 R478 V479 G480 Q481 S482 M483 R580 L582 Y583
Binding residue
(residue number reindexed from 1)		F138 R442 V443 G444 Q445 S446 M447 R544 L546 Y547
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) W241 C277 H335 D358 Y516
Catalytic site (residue number reindexed from 1) W205 C241 H299 D322 Y480
Enzyme Commision number 2.3.1.-
2.3.2.13: protein-glutamine gamma-glutamyltransferase.
3.4.-.-
3.5.1.44: protein-glutamine glutaminase.
Gene Ontology
Molecular Function
GO:0003810 protein-glutamine gamma-glutamyltransferase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008233 peptidase activity
GO:0016746 acyltransferase activity
GO:0046872 metal ion binding
GO:0050568 protein-glutamine glutaminase activity
GO:0120294 peptide serotonyltransferase activity
GO:0120295 histone serotonyltransferase activity
GO:0120296 peptide dopaminyltransferase activity
GO:0120297 histone dopaminyltransferase activity
GO:0120298 peptide noradrenalinyltransferase activity
GO:0120299 peptide histaminyltransferase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006508 proteolysis
GO:0007200 phospholipase C-activating G protein-coupled receptor signaling pathway
GO:0010467 gene expression
GO:0014046 dopamine secretion
GO:0018149 peptide cross-linking
GO:0018277 protein deamination
GO:0032471 negative regulation of endoplasmic reticulum calcium ion concentration
GO:0042981 regulation of apoptotic process
GO:0043065 positive regulation of apoptotic process
GO:0043277 apoptotic cell clearance
GO:0043547 positive regulation of GTPase activity
GO:0045785 positive regulation of cell adhesion
GO:0050769 positive regulation of neurogenesis
GO:0051057 positive regulation of small GTPase mediated signal transduction
GO:0051561 positive regulation of mitochondrial calcium ion concentration
GO:0060348 bone development
GO:0060445 branching involved in salivary gland morphogenesis
GO:0060662 salivary gland cavitation
GO:0071314 cellular response to cocaine
GO:1903351 cellular response to dopamine
GO:1903672 positive regulation of sprouting angiogenesis
GO:1904015 cellular response to serotonin
GO:2000425 regulation of apoptotic cell clearance
Cellular Component
GO:0000785 chromatin
GO:0000786 nucleosome
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0031012 extracellular matrix
GO:0048471 perinuclear region of cytoplasm
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kv3, PDBe:1kv3, PDBj:1kv3
PDBsum1kv3
PubMed11867708
UniProtP21980|TGM2_HUMAN Protein-glutamine gamma-glutamyltransferase 2 (Gene Name=TGM2)

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