Structure of PDB 1ggy Chain B Binding Site BS01

Receptor Information
>1ggy Chain B (length=705) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FGGRRAVPPNNSNAAEDDLPTVELQGQEFLNVTSVHLFKERWDTNKVDHH
TDKYENNKLIVRRGQSFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGT
YIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMYVAVWT
PYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYG
EVNDIKTRSWSYGQFEDGILDTCLYVMDRAQMDLSGRGNPIKVSRVGSAM
VNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCW
VFAGVFNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLT
KDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQENSDGMYRCGPASVQ
AIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIV
TKQIGGDGMMDITDTYKFQEGQEEERLALETALMYGAKKPLNTSNVDMDF
EVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFYTGVPKAEFKKET
FDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQ
KSTVLTIPEIIIKVRGTQVVGSDMTVTVEFTNPLKETLRNVWVHLDGPGV
TRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGELD
VQIQR
Ligand information
Ligand IDYB
InChIInChI=1S/Yb/q+3
InChIKeyAWSFICBXMUKWSK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341
OpenEye OEToolkits 1.5.0		[Yb+3]
FormulaYb
NameYTTERBIUM (III) ION
ChEMBL
DrugBank
ZINC
PDB chain1ggy Chain B Residue 732 [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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PDB1ggy Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N436 E485 E490
Binding residue
(residue number reindexed from 1)		N421 E470 E475
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) W279 C314 H373 D396 Y560
Catalytic site (residue number reindexed from 1) W264 C299 H358 D381 Y538
Enzyme Commision number 2.3.2.13: protein-glutamine gamma-glutamyltransferase.
Gene Ontology
Molecular Function
GO:0003810 protein-glutamine gamma-glutamyltransferase activity
GO:0005515 protein binding
GO:0016746 acyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0007596 blood coagulation
GO:0018149 peptide cross-linking
GO:0072378 blood coagulation, fibrin clot formation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0031093 platelet alpha granule lumen
GO:0062023 collagen-containing extracellular matrix
GO:0072562 blood microparticle
GO:1990234 transferase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ggy, PDBe:1ggy, PDBj:1ggy
PDBsum1ggy
PubMed9988734
UniProtP00488|F13A_HUMAN Coagulation factor XIII A chain (Gene Name=F13A1)

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