Structure of PDB 4dur Chain B Binding Site BS03

Receptor Information
>4dur Chain B (length=754) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLDDYVNTQGASLFSVTKKQLGAGSIEECAAKCEEDEEFTCRAFQYHSKE
QQCVIMAENRKSSIIIRMRDVVLFEKKVYLSECKTGNGKNYRGTMSKTKN
GITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPE
KRYDYCDILECEEECMHCSGENYDGKISKTMSGLECQAWDSQSPHAHGYI
PSKFPNKNLKKNYCRNPDRELRPWCFTTDPNKRWELCDIPRCTTPPPSSG
PTYQCLKGTGENYRGNVAVTVSGHTCQHWSAQTPHTHNRTPENFPCKNLD
ENYCRNPDGKRAPWCHTTNSQVRWEYCKIPSCDPTAPPELTPVVQDCYHG
DGQSYRGTSSTTTTGKKCQSWSSMTPHRHQKTPENYPNAGLTMNYCRNPD
ADKGPWCFTTDPSVRWEYCNLKKCSGTEASVVAPPPDCMFGNYRGKTTVT
GTPCQDWAAQEPHRHSIFTPETNPLEKNYCRNPDGDVGGPWCYTTNPRKL
YDYCDVPQCPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFG
MHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIE
VSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITG
WGETFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSC
QGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGV
MRNN
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 chain4dur Chain B Residue 805 [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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PDB4dur The X-ray crystal structure of full-length human plasminogen
Resolution2.45 Å
Binding residue
(original residue number in PDB)		I682 G739
Binding residue
(residue number reindexed from 1)		I648 G702
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H603 D646 Q738 G739 D740 S741 G742
Catalytic site (residue number reindexed from 1) H569 D612 Q701 G702 D703 S704 G705
Enzyme Commision number 3.4.21.7: plasmin.
Gene Ontology
Molecular Function
GO:0002020 protease binding
GO:0004175 endopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005102 signaling receptor binding
GO:0005515 protein binding
GO:0008236 serine-type peptidase activity
GO:0019899 enzyme binding
GO:0019900 kinase binding
GO:0019904 protein domain specific binding
GO:0034185 apolipoprotein binding
GO:0051087 protein-folding chaperone binding
GO:1990405 protein antigen binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation
GO:0008285 negative regulation of cell population proliferation
GO:0010812 negative regulation of cell-substrate adhesion
GO:0016485 protein processing
GO:0022617 extracellular matrix disassembly
GO:0042246 tissue regeneration
GO:0042730 fibrinolysis
GO:0043536 positive regulation of blood vessel endothelial cell migration
GO:0045445 myoblast differentiation
GO:0046716 muscle cell cellular homeostasis
GO:0048771 tissue remodeling
GO:0051702 biological process involved in interaction with symbiont
GO:0051918 negative regulation of fibrinolysis
GO:0051919 positive regulation of fibrinolysis
GO:0060707 trophoblast giant cell differentiation
GO:0060716 labyrinthine layer blood vessel development
GO:0071674 mononuclear cell migration
GO:0099183 trans-synaptic signaling by BDNF, modulating synaptic transmission
GO:2000048 negative regulation of cell-cell adhesion mediated by cadherin
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0031093 platelet alpha granule lumen
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome
GO:0072562 blood microparticle
GO:0098685 Schaffer collateral - CA1 synapse
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4dur, PDBe:4dur, PDBj:4dur
PDBsum4dur
PubMed22832192
UniProtP00747|PLMN_HUMAN Plasminogen (Gene Name=PLG)

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