5LY1
JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-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 | HOH662 |
| A | HOH671 |
| 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 | 4 |
| Details | binding site for residue CL A 503 |
| Chain | Residue |
| A | PHE227 |
| A | PRO228 |
| A | GLY229 |
| B | LYS105 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue GOL A 504 |
| Chain | Residue |
| A | GLU23 |
| A | TYR33 |
| A | PHE353 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue PPI A 505 |
| Chain | Residue |
| A | GLY170 |
| A | TYR177 |
| A | SER288 |
| A | ASN290 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue NI B 501 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | HOH632 |
| B | HOH670 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 502 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue GOL B 503 |
| Chain | Residue |
| B | GLU23 |
| B | TYR33 |
| B | PHE353 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 504 |
| Chain | Residue |
| B | ARG25 |
| B | PHE27 |
| B | ASP146 |
| B | GLU147 |
| B | TRP148 |
| B | ASN149 |
| B | ARG152 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue PPI B 505 |
| Chain | Residue |
| B | GLY170 |
| B | TYR177 |
| B | GLU190 |
| B | SER288 |
| B | HOH632 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue GOL C 401 |
| Chain | Residue |
| C | GLU23 |
| C | TYR33 |
| C | HOH563 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue NI C 402 |
| Chain | Residue |
| C | HIS188 |
| C | GLU190 |
| C | HIS276 |
| C | HOH508 |
| C | HOH556 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 403 |
| Chain | Residue |
| C | CYS234 |
| C | HIS240 |
| C | CYS306 |
| C | CYS308 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue CL C 404 |
| Chain | Residue |
| C | PHE227 |
| C | GLY229 |
| C | SER230 |
| D | LYS105 |
| site_id | AD6 |
| Number of Residues | 8 |
| Details | binding site for residue GOL C 405 |
| Chain | Residue |
| C | ASP193 |
| C | TYR273 |
| C | TYR299 |
| C | GLN302 |
| C | ILE341 |
| C | HIS343 |
| C | HOH528 |
| C | HOH592 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue NI D 501 |
| Chain | Residue |
| D | HIS188 |
| D | GLU190 |
| D | HIS276 |
| D | HOH677 |
| D | HOH684 |
| D | HOH694 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 502 |
| Chain | Residue |
| D | CYS234 |
| D | HIS240 |
| D | CYS306 |
| D | CYS308 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue CL D 503 |
| Chain | Residue |
| D | PHE227 |
| D | PRO228 |
| D | GLY229 |
| D | SER230 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue PPI D 504 |
| Chain | Residue |
| D | GLY170 |
| D | TYR177 |
| D | GLU190 |
| D | SER288 |
| D | ASN290 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for Di-peptide 48V E 0 and THR E 13 |
| Chain | Residue |
| D | ASN86 |
| D | ILE87 |
| D | GLN88 |
| E | DTY1 |
| E | TYR12 |
| site_id | AE3 |
| Number of Residues | 7 |
| Details | binding site for Di-peptide 48V E 0 and DTY E 1 |
| Chain | Residue |
| D | GLN88 |
| D | LYS89 |
| D | LYS90 |
| E | VAL2 |
| E | TRP11 |
| E | TYR12 |
| E | THR13 |
| site_id | AE4 |
| Number of Residues | 9 |
| Details | binding site for Di-peptide DTY E 1 and VAL E 2 |
| Chain | Residue |
| C | ARG309 |
| D | GLN88 |
| D | LYS89 |
| D | LYS90 |
| E | 48V0 |
| E | TYR3 |
| E | ARG10 |
| E | TRP11 |
| E | TYR12 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 168 |
| Details | Domain: {"description":"JmjN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00537","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 498 |
| Details | Domain: {"description":"JmjC","evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| 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 | 4 |
| 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 | 16 |
| 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 | 4 |
| 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 |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| C | GLY170 | hydrogen bond acceptor, steric role |
| C | TYR177 | hydrogen bond donor, steric role |
| C | HIS188 | metal ligand |
| C | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| C | HIS276 | metal ligand |
| C | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA4 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| D | GLY170 | hydrogen bond acceptor, steric role |
| D | TYR177 | hydrogen bond donor, steric role |
| D | HIS188 | metal ligand |
| D | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| D | HIS276 | metal ligand |
| D | SER288 | hydrogen bond donor, steric role |
