Structure of PDB 7n88 Chain B Binding Site BS04

Receptor Information
>7n88 Chain B (length=688) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSVQWCAVSQPEATKCFQWQRNMRKVRGPPVSCIKRDSPIQCIQAIAENR
ADAVTLDGGFIYEAGLAPYKLRPVAAEVYGTERQPRTHYYAVAVVKKGGS
FQLNELQGLKSCHTGLRRTAGWNVPIGTLRPFLNWTGPPEPIEAAVARFF
SASCVPGADKGQFPNLCRLCAGTGENKCAFSSQEPYFSYSGAFKCLRDGA
GDVAFIRESTVFEDLSDEAERDEYELLCPDNTRKPVDKFKDCHLARVPSH
AVVARSVNGKEDAIWNLLRQAQEKFGKDKSPKFQLFGSPSGQKDLLFKDS
AIGFSRVPPRIDSGLYLGSGYFTAIQNLRKSEEEVAARRARVVWCAVGEQ
ELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAG
KCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYLAVAVVRRSDTSLTWNSV
KGKKSCHTAVDRTAGWNIPMGLLFNQTGSCKFDEYFSQSCAPGSDPRSNL
CALCIGDEQGENKCVPNSNERYYGYTGAFRCLAENAGDVAFVKDVTVLQN
TDGNNNEAWAKDLKLADFALLCLDGKRKPVTEARSCHLAMAPNHAVVSRM
DKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARL
HGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK
Ligand information
Ligand IDBCT
InChIInChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1
InChIKeyBVKZGUZCCUSVTD-UHFFFAOYSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(=O)(O)[O-]
CACTVS 3.341OC([O-])=O
ACDLabs 10.04[O-]C(=O)O
FormulaC H O3
NameBICARBONATE ION
ChEMBL
DrugBank
ZINC
PDB chain7n88 Chain B Residue 704 [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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PDB7n88 Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		D61 Y93 R122 A124 Y193
Binding residue
(residue number reindexed from 1)		D57 Y89 R118 A120 Y189
Annotation score4
Enzymatic activity
Enzyme Commision number 3.4.21.-
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0003677 DNA binding
GO:0004252 serine-type endopeptidase activity
GO:0004869 cysteine-type endopeptidase inhibitor activity
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0008201 heparin binding
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
GO:0043539 protein serine/threonine kinase activator activity
GO:0046872 metal ion binding
GO:0140912 membrane destabilizing activity
Biological Process
GO:0001503 ossification
GO:0001817 regulation of cytokine production
GO:0002227 innate immune response in mucosa
GO:0002376 immune system process
GO:0006508 proteolysis
GO:0006826 iron ion transport
GO:0006959 humoral immune response
GO:0019731 antibacterial humoral response
GO:0019732 antifungal humoral response
GO:0031640 killing of cells of another organism
GO:0031665 negative regulation of lipopolysaccharide-mediated signaling pathway
GO:0032680 regulation of tumor necrosis factor production
GO:0032780 negative regulation of ATP-dependent activity
GO:0033690 positive regulation of osteoblast proliferation
GO:0034145 positive regulation of toll-like receptor 4 signaling pathway
GO:0042742 defense response to bacterium
GO:0043066 negative regulation of apoptotic process
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0044793 negative regulation by host of viral process
GO:0045071 negative regulation of viral genome replication
GO:0045669 positive regulation of osteoblast differentiation
GO:0048525 negative regulation of viral process
GO:0050829 defense response to Gram-negative bacterium
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0060349 bone morphogenesis
GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0071902 positive regulation of protein serine/threonine kinase activity
GO:1900159 positive regulation of bone mineralization involved in bone maturation
GO:1900229 negative regulation of single-species biofilm formation in or on host organism
GO:1902732 positive regulation of chondrocyte proliferation
GO:2000117 negative regulation of cysteine-type endopeptidase activity
GO:2000308 negative regulation of tumor necrosis factor (ligand) superfamily member 11 production
GO:2001205 negative regulation of osteoclast development
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005769 early endosome
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0030141 secretory granule
GO:0032991 protein-containing complex
GO:0035580 specific granule lumen
GO:0042581 specific granule
GO:0055037 recycling endosome
GO:0070062 extracellular exosome
GO:0097013 phagocytic vesicle lumen
GO:1904724 tertiary granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7n88, PDBe:7n88, PDBj:7n88
PDBsum7n88
PubMed34751649
UniProtP02788|TRFL_HUMAN Lactotransferrin (Gene Name=LTF)

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