6H8P
JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue NI A 501 |
| Chain | Residue |
| A | HIS188 |
| A | GLU190 |
| A | HIS276 |
| A | OGA504 |
| A | HOH713 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 502 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue CL A 503 |
| Chain | Residue |
| A | PHE227 |
| A | GLY229 |
| A | SER230 |
| site_id | AC4 |
| Number of Residues | 12 |
| Details | binding site for residue OGA A 504 |
| Chain | Residue |
| A | TYR132 |
| A | PHE185 |
| A | HIS188 |
| A | GLU190 |
| A | SER196 |
| A | ASN198 |
| A | LYS206 |
| A | HIS276 |
| A | SER288 |
| A | NI501 |
| A | HOH713 |
| C | M3L26 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue GOL A 505 |
| Chain | Residue |
| A | TYR59 |
| A | ARG98 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue GOL A 506 |
| Chain | Residue |
| A | GLU23 |
| A | ARG29 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 507 |
| Chain | Residue |
| A | LYS217 |
| A | TYR273 |
| A | TYR299 |
| A | GLN302 |
| A | ILE341 |
| A | HIS343 |
| A | HOH610 |
| A | HOH627 |
| A | HOH669 |
| A | HOH733 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue NI B 501 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | OGA504 |
| B | HOH677 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 502 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue CL B 503 |
| Chain | Residue |
| A | LYS105 |
| B | PHE227 |
| B | GLY229 |
| B | SER230 |
| site_id | AD2 |
| Number of Residues | 12 |
| Details | binding site for residue OGA B 504 |
| Chain | Residue |
| B | TYR132 |
| B | PHE185 |
| B | HIS188 |
| B | GLU190 |
| B | SER196 |
| B | ASN198 |
| B | LYS206 |
| B | HIS276 |
| B | NI501 |
| B | HOH677 |
| B | HOH748 |
| D | M3L26 |
| site_id | AD3 |
| Number of Residues | 1 |
| Details | binding site for residue GOL B 505 |
| Chain | Residue |
| B | ARG98 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 84 |
| Details | Domain: {"description":"JmjN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00537","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 332 |
| Details | Domain: {"description":"JmjC","evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"5F2W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F32","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F37","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F39","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F5I","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"B2RXH2","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"19144645","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"3782055","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| A | GLY170 | hydrogen bond acceptor, steric role |
| A | TYR177 | hydrogen bond donor, steric role |
| A | HIS188 | metal ligand |
| A | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| A | HIS276 | metal ligand |
| A | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| B | GLY170 | hydrogen bond acceptor, steric role |
| B | TYR177 | hydrogen bond donor, steric role |
| B | HIS188 | metal ligand |
| B | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| B | HIS276 | metal ligand |
| B | SER288 | hydrogen bond donor, steric role |
