6G5W
Crystal Structure of KDM4A with compound YP-03-038
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue NI A 402 |
| Chain | Residue |
| A | HIS215 |
| A | HOH707 |
| A | HOH712 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue NI A 403 |
| Chain | Residue |
| A | HIS276 |
| A | CIT406 |
| A | HOH502 |
| A | HOH571 |
| A | HIS188 |
| A | GLU190 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | GLU235 |
| A | ALA236 |
| A | PHE237 |
| A | LEU238 |
| A | HOH511 |
| A | HOH525 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | THR139 |
| A | TYR141 |
| A | HOH518 |
| A | HOH607 |
| A | HOH714 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | binding site for residue CIT A 406 |
| Chain | Residue |
| A | TYR132 |
| A | TYR177 |
| A | PHE185 |
| A | HIS188 |
| A | ASN198 |
| A | LYS206 |
| A | TRP208 |
| A | HIS276 |
| A | ALA286 |
| A | NI403 |
| A | HOH502 |
| A | HOH560 |
| A | HOH571 |
| A | HOH573 |
| A | HOH603 |
| A | HOH667 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for residue CIT A 407 |
| Chain | Residue |
| A | GLU214 |
| A | HIS215 |
| A | ARG218 |
| A | HOH506 |
| A | HOH568 |
| B | GLU115 |
| B | LYS259 |
| B | NI403 |
| B | ENZ407 |
| B | HOH661 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue NI B 402 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | CIT406 |
| B | HOH501 |
| B | HOH544 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue NI B 403 |
| Chain | Residue |
| A | CIT407 |
| B | ENZ407 |
| B | HOH661 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue NA B 404 |
| Chain | Residue |
| B | ASN26 |
| B | SER28 |
| B | HOH651 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| A | ARG95 |
| B | TYR59 |
| B | ARG98 |
| B | PHE283 |
| site_id | AD4 |
| Number of Residues | 16 |
| Details | binding site for residue CIT B 406 |
| Chain | Residue |
| B | TYR132 |
| B | TYR177 |
| B | PHE185 |
| B | HIS188 |
| B | ASN198 |
| B | LYS206 |
| B | TRP208 |
| B | HIS276 |
| B | ALA286 |
| B | NI402 |
| B | HOH501 |
| B | HOH537 |
| B | HOH544 |
| B | HOH623 |
| B | HOH631 |
| B | HOH647 |
| site_id | AD5 |
| Number of Residues | 14 |
| Details | binding site for residue ENZ B 407 |
| Chain | Residue |
| B | HOH661 |
| A | HIS215 |
| A | CIT407 |
| B | PHE114 |
| B | GLU115 |
| B | GLU118 |
| B | SER207 |
| B | TRP208 |
| B | TYR209 |
| B | LYS259 |
| B | VAL260 |
| B | THR261 |
| B | NI403 |
| B | HOH634 |
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 |
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 |
