5F3I
Crystal structure of human KDM4A in complex with compound 54j
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | binding site for residue ZN A 401 |
Chain | Residue |
A | HIS188 |
A | GLU190 |
A | HIS276 |
A | 5UJ403 |
A | HOH511 |
site_id | AC2 |
Number of Residues | 4 |
Details | binding site for residue ZN A 402 |
Chain | Residue |
A | CYS234 |
A | HIS240 |
A | CYS306 |
A | CYS308 |
site_id | AC3 |
Number of Residues | 13 |
Details | binding site for residue 5UJ A 403 |
Chain | Residue |
A | TYR132 |
A | ASP135 |
A | TYR177 |
A | PHE185 |
A | HIS188 |
A | GLU190 |
A | LYS206 |
A | TRP208 |
A | LYS241 |
A | HIS276 |
A | ZN401 |
A | HOH511 |
A | HOH571 |
site_id | AC4 |
Number of Residues | 2 |
Details | binding site for residue DMS A 404 |
Chain | Residue |
A | TRP332 |
A | LYS333 |
site_id | AC5 |
Number of Residues | 4 |
Details | binding site for residue ZN B 401 |
Chain | Residue |
B | HIS188 |
B | GLU190 |
B | HIS276 |
B | 5UJ403 |
site_id | AC6 |
Number of Residues | 4 |
Details | binding site for residue ZN B 402 |
Chain | Residue |
B | CYS234 |
B | HIS240 |
B | CYS306 |
B | CYS308 |
site_id | AC7 |
Number of Residues | 14 |
Details | binding site for residue 5UJ B 403 |
Chain | Residue |
B | TYR132 |
B | ASP135 |
B | TYR175 |
B | TYR177 |
B | PHE185 |
B | HIS188 |
B | GLU190 |
B | LYS206 |
B | TRP208 |
B | LYS241 |
B | HIS276 |
B | VAL313 |
B | ZN401 |
B | HOH588 |
site_id | AC8 |
Number of Residues | 11 |
Details | binding site for residue GOL B 404 |
Chain | Residue |
B | VAL75 |
B | THR76 |
B | GLY77 |
B | THR126 |
B | PHE127 |
B | HOH573 |
D | VAL75 |
D | THR76 |
D | GLY77 |
D | THR126 |
D | PHE127 |
site_id | AC9 |
Number of Residues | 1 |
Details | binding site for residue DMS B 405 |
Chain | Residue |
B | ARG294 |
site_id | AD1 |
Number of Residues | 5 |
Details | binding site for residue ZN C 401 |
Chain | Residue |
C | HIS188 |
C | GLU190 |
C | HIS276 |
C | 5UJ403 |
C | HOH504 |
site_id | AD2 |
Number of Residues | 4 |
Details | binding site for residue ZN C 402 |
Chain | Residue |
C | CYS234 |
C | HIS240 |
C | CYS306 |
C | CYS308 |
site_id | AD3 |
Number of Residues | 14 |
Details | binding site for residue 5UJ C 403 |
Chain | Residue |
C | TYR132 |
C | GLU169 |
C | TYR175 |
C | TYR177 |
C | PHE185 |
C | HIS188 |
C | GLU190 |
C | ASP191 |
C | LYS206 |
C | TRP208 |
C | LYS241 |
C | HIS276 |
C | ZN401 |
C | HOH504 |
site_id | AD4 |
Number of Residues | 5 |
Details | binding site for residue ZN D 401 |
Chain | Residue |
D | HIS188 |
D | GLU190 |
D | HIS276 |
D | 5UJ403 |
D | HOH505 |
site_id | AD5 |
Number of Residues | 4 |
Details | binding site for residue ZN D 402 |
Chain | Residue |
D | CYS234 |
D | HIS240 |
D | CYS306 |
D | CYS308 |
site_id | AD6 |
Number of Residues | 11 |
Details | binding site for residue 5UJ D 403 |
Chain | Residue |
D | ZN401 |
D | HOH505 |
D | TYR132 |
D | TYR177 |
D | PHE185 |
D | HIS188 |
D | GLU190 |
D | LYS206 |
D | TRP208 |
D | LYS241 |
D | HIS276 |
site_id | AD7 |
Number of Residues | 3 |
Details | binding site for residue DMS D 404 |
Chain | Residue |
D | ALA231 |
D | GLN232 |
D | GLU235 |
site_id | AD8 |
Number of Residues | 1 |
Details | binding site for residue DMS D 405 |
Chain | Residue |
D | PHE257 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:16677698 |
Chain | Residue | Details |
A | TYR132 | |
D | TYR132 | |
D | ASN198 | |
D | LYS206 | |
A | ASN198 | |
A | LYS206 | |
B | TYR132 | |
B | ASN198 | |
B | LYS206 | |
C | TYR132 | |
C | ASN198 | |
C | LYS206 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00538, ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
Chain | Residue | Details |
A | HIS188 | |
A | HIS276 | |
B | HIS188 | |
B | HIS276 | |
C | HIS188 | |
C | HIS276 | |
D | HIS188 | |
D | HIS276 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
Chain | Residue | Details |
A | GLU190 | |
B | GLU190 | |
C | GLU190 | |
D | GLU190 |
site_id | SWS_FT_FI4 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0007744|PDB:5F2W, ECO:0007744|PDB:5F32, ECO:0007744|PDB:5F37, ECO:0007744|PDB:5F39, ECO:0007744|PDB:5F3E, ECO:0007744|PDB:5F3G, ECO:0007744|PDB:5F5I |
Chain | Residue | Details |
A | CYS234 | |
C | HIS240 | |
C | CYS306 | |
C | CYS308 | |
D | CYS234 | |
D | HIS240 | |
D | CYS306 | |
D | CYS308 | |
A | HIS240 | |
A | CYS306 | |
A | CYS308 | |
B | CYS234 | |
B | HIS240 | |
B | CYS306 | |
B | CYS308 | |
C | CYS234 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000250|UniProtKB:B2RXH2 |
Chain | Residue | Details |
A | LYS241 | |
B | LYS241 | |
C | LYS241 | |
D | LYS241 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | MOD_RES: N-acetylalanine => ECO:0007744|PubMed:19413330 |
Chain | Residue | Details |
A | ALA2 | |
B | ALA2 | |
C | ALA2 | |
D | ALA2 |
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 |