1WDA
Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0002376 | biological_process | immune system process |
| A | 0004668 | molecular_function | protein-arginine deiminase activity |
| A | 0005509 | molecular_function | calcium ion binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006334 | biological_process | nucleosome assembly |
| A | 0006338 | biological_process | chromatin remodeling |
| A | 0006351 | biological_process | DNA-templated transcription |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0019827 | biological_process | stem cell population maintenance |
| A | 0031452 | biological_process | negative regulation of heterochromatin formation |
| A | 0032991 | cellular_component | protein-containing complex |
| A | 0036211 | biological_process | protein modification process |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0043687 | biological_process | post-translational protein modification |
| A | 0045087 | biological_process | innate immune response |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051081 | biological_process | nuclear membrane disassembly |
| A | 0140645 | biological_process | neutrophil extracellular trap formation |
| A | 0140794 | molecular_function | histone arginine deiminase activity |
| A | 0140795 | molecular_function | histone H3R2 arginine deiminase activity |
| A | 0140796 | molecular_function | histone H3R8 arginine deiminase activity |
| A | 0140797 | molecular_function | histone H3R17 arginine deiminase activity |
| A | 0140798 | molecular_function | histone H3R26 arginine deiminase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA A 900 |
| Chain | Residue |
| A | GLN349 |
| A | GLU353 |
| A | PHE407 |
| A | LEU410 |
| A | GLU411 |
| A | HOH919 |
| A | HOH942 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 901 |
| Chain | Residue |
| A | ASP157 |
| A | ASP165 |
| A | ASP176 |
| A | ASP179 |
| A | ASN153 |
| A | ASP155 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CA A 902 |
| Chain | Residue |
| A | ASP155 |
| A | ASP157 |
| A | ASP179 |
| A | ASP388 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CA A 903 |
| Chain | Residue |
| A | GLU351 |
| A | ASP369 |
| A | SER370 |
| A | ASN373 |
| A | HOH1065 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CA A 904 |
| Chain | Residue |
| A | ASP165 |
| A | ASP168 |
| A | GLU170 |
| A | HOH1059 |
| A | HOH1066 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 905 |
| Chain | Residue |
| A | SER402 |
| A | GLY403 |
| A | ARG441 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 906 |
| Chain | Residue |
| A | ARG495 |
| A | SER496 |
| A | LYS499 |
| A | LYS615 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 A 907 |
| Chain | Residue |
| A | LYS525 |
| A | ASN528 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE BAG A 801 |
| Chain | Residue |
| A | TRP347 |
| A | GLN349 |
| A | ASP350 |
| A | ARG374 |
| A | GLY408 |
| A | HIS471 |
| A | ASP473 |
| A | ASN588 |
| A | ARG639 |
| A | HIS640 |
| A | ALA645 |
| A | HOH941 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"evidences":[{"source":"PubMed","id":"15247907","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"15247907","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17002273","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"21882827","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 5 |
| Details | Modified residue: {"description":"Citrulline","evidences":[{"source":"PubMed","id":"20201080","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1wd8 |
| Chain | Residue | Details |
| A | ASP473 | |
| A | ASP350 | |
| A | ALA645 | |
| A | HIS471 |
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 594 |
| Chain | Residue | Details |
| A | ASP350 | electrostatic stabiliser |
| A | HIS471 | proton acceptor, proton donor |
| A | ASP473 | electrostatic stabiliser |
| A | ALA645 | nucleofuge, nucleophile, proton acceptor, proton donor |
