3GIS
Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004252 | molecular_function | serine-type endopeptidase activity |
| A | 0005576 | cellular_component | extracellular region |
| A | 0006508 | biological_process | proteolysis |
| A | 0007596 | biological_process | blood coagulation |
| B | 0004252 | molecular_function | serine-type endopeptidase activity |
| B | 0005509 | molecular_function | calcium ion binding |
| B | 0006508 | biological_process | proteolysis |
| B | 0007596 | biological_process | blood coagulation |
| C | 0004252 | molecular_function | serine-type endopeptidase activity |
| C | 0005576 | cellular_component | extracellular region |
| C | 0006508 | biological_process | proteolysis |
| C | 0007596 | biological_process | blood coagulation |
| D | 0004252 | molecular_function | serine-type endopeptidase activity |
| D | 0005509 | molecular_function | calcium ion binding |
| D | 0006508 | biological_process | proteolysis |
| D | 0007596 | biological_process | blood coagulation |
| E | 0004252 | molecular_function | serine-type endopeptidase activity |
| E | 0005576 | cellular_component | extracellular region |
| E | 0006508 | biological_process | proteolysis |
| E | 0007596 | biological_process | blood coagulation |
| F | 0004252 | molecular_function | serine-type endopeptidase activity |
| F | 0005509 | molecular_function | calcium ion binding |
| F | 0006508 | biological_process | proteolysis |
| F | 0007596 | biological_process | blood coagulation |
| X | 0004888 | molecular_function | transmembrane signaling receptor activity |
| X | 0005509 | molecular_function | calcium ion binding |
| X | 0016020 | cellular_component | membrane |
| Y | 0004888 | molecular_function | transmembrane signaling receptor activity |
| Y | 0005509 | molecular_function | calcium ion binding |
| Y | 0016020 | cellular_component | membrane |
| Z | 0004888 | molecular_function | transmembrane signaling receptor activity |
| Z | 0005509 | molecular_function | calcium ion binding |
| Z | 0016020 | cellular_component | membrane |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 16 |
| Chain | Residue |
| A | ALA1 |
| A | GLU1 |
| A | GLY1 |
| A | SER1 |
| A | HOH384 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 17 |
| Chain | Residue |
| A | ARG1 |
| A | ASN1 |
| A | HOH111 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1 |
| Chain | Residue |
| B | ASP125 |
| B | ARG126 |
| B | PHE232 |
| B | LYS235 |
| A | PHE1 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 2 |
| Chain | Residue |
| B | ARG101 |
| B | ASN179 |
| B | HOH558 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 11 |
| Chain | Residue |
| B | ALA132 |
| B | GLU164 |
| B | ARG165 |
| B | PRO166 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 13 |
| Chain | Residue |
| B | TRP96 |
| B | ARG97 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 14 |
| Chain | Residue |
| B | ARG101 |
| B | HOH515 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 16 |
| Chain | Residue |
| B | HOH250 |
| C | ARG14 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 3 |
| Chain | Residue |
| C | PHE1 |
| D | ASP125 |
| D | ARG126 |
| D | LYS235 |
| D | HOH440 |
| D | HOH525 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 4 |
| Chain | Residue |
| D | ARG93 |
| D | ARG101 |
| D | ASN179 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 5 |
| Chain | Residue |
| D | GLU164 |
| D | ARG165 |
| D | PRO166 |
| D | HOH266 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 D 6 |
| Chain | Residue |
| A | ARG14 |
| D | LYS169 |
| D | ARG175 |
| D | HOH350 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 E 16 |
| Chain | Residue |
| E | ALA1 |
| E | GLY1 |
| E | SER1 |
| E | HOH313 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 F 7 |
| Chain | Residue |
| F | ASP125 |
| F | ARG126 |
| F | LYS235 |
| F | HOH291 |
| site_id | BC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA X 1001 |
| Chain | Residue |
| X | HOH148 |
| X | ASP423 |
| X | ILE424 |
| X | GLU426 |
| X | ASN439 |
| X | LEU440 |
| X | THR443 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA Y 1002 |
| Chain | Residue |
| Y | ASP423 |
| Y | ILE424 |
| Y | GLU426 |
| Y | ASN439 |
| Y | LEU440 |
| Y | THR443 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA Z 1003 |
| Chain | Residue |
| Z | HOH256 |
| Z | ASP423 |
| Z | ILE424 |
| Z | GLU426 |
| Z | ASN439 |
| Z | LEU440 |
| Z | THR443 |
Functional Information from PROSITE/UniProt
| site_id | PS00010 |
| Number of Residues | 12 |
| Details | ASX_HYDROXYL Aspartic acid and asparagine hydroxylation site. ChNlpgtFeCiC |
| Chain | Residue | Details |
| X | CYS437-CYS448 |
| site_id | PS00134 |
| Number of Residues | 6 |
| Details | TRYPSIN_HIS Serine proteases, trypsin family, histidine active site. LTAAHC |
| Chain | Residue | Details |
| B | LEU53-CYS58 |
| site_id | PS01186 |
| Number of Residues | 15 |
| Details | EGF_2 EGF-like domain signature 2. CeCpeGYilddgfi.C |
| Chain | Residue | Details |
| X | CYS407-CYS421 |
| site_id | PS01187 |
| Number of Residues | 24 |
| Details | EGF_CA Calcium-binding EGF-like domain signature. DiDECenggf.........Csgv....ChNlpgtFeC |
| Chain | Residue | Details |
| X | ASP423-CYS446 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 66 |
| Details | Region: {"description":"High affinity receptor-binding region which is also known as the TP508 peptide"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 9 |
| Details | Active site: {"description":"Charge relay system"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| Details | Glycosylation: {"description":"N-linked (GlcNAc...) (complex) asparagine","evidences":[{"source":"PubMed","id":"16335952","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19139490","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19838169","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"873923","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 120 |
| Details | Domain: {"description":"EGF-like 6; calcium-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00076","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 36 |
| Details | Domain: {"description":"EGF-like 5","evidences":[{"source":"PROSITE-ProRule","id":"PRU00076","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| B | ASP102 | |
| B | HIS57 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| B | ALA195 | |
| B | GLY193 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| D | ALA195 | |
| D | GLY193 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| F | ALA195 | |
| F | GLY193 |
| site_id | CSA13 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| B | ALA195 | |
| B | GLY196 |
| site_id | CSA14 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| D | ALA195 | |
| D | GLY196 |
| site_id | CSA15 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| F | ALA195 | |
| F | GLY196 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| D | ASP102 | |
| D | HIS57 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| F | ASP102 | |
| F | HIS57 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| B | ASP102 | |
| B | ALA195 | |
| B | HIS57 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| D | ASP102 | |
| D | ALA195 | |
| D | HIS57 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| F | ASP102 | |
| F | ALA195 | |
| F | HIS57 |
| site_id | CSA7 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| B | ASP102 | |
| B | ALA195 | |
| B | GLY193 | |
| B | HIS57 |
| site_id | CSA8 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| D | ASP102 | |
| D | ALA195 | |
| D | GLY193 | |
| D | HIS57 |
| site_id | CSA9 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1a0j |
| Chain | Residue | Details |
| F | ASP102 | |
| F | ALA195 | |
| F | GLY193 | |
| F | HIS57 |
