5FYI
Crystal structure of human JMJD2A in complex with pyruvate
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 | PYR1355 |
| A | HOH2083 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI B 501 |
| Chain | Residue |
| B | HOH2090 |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | PYR1354 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 502 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PYR A 1355 |
| Chain | Residue |
| A | PHE185 |
| A | HIS188 |
| A | GLU190 |
| A | SER196 |
| A | ASN198 |
| A | TRP208 |
| A | HIS276 |
| A | NI501 |
| A | PYR1356 |
| site_id | AC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PYR B 1354 |
| Chain | Residue |
| B | PHE185 |
| B | HIS188 |
| B | GLU190 |
| B | SER196 |
| B | ASN198 |
| B | TRP208 |
| B | HIS276 |
| B | NI501 |
| B | PYR1355 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PYR B 1355 |
| Chain | Residue |
| B | TYR132 |
| B | TYR177 |
| B | PHE185 |
| B | ASN198 |
| B | LYS206 |
| B | SER288 |
| B | PYR1354 |
| B | EDO1364 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PYR A 1356 |
| Chain | Residue |
| A | TYR132 |
| A | TYR177 |
| A | ASN198 |
| A | LYS206 |
| A | SER288 |
| A | PYR1355 |
| A | EDO1365 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 3000 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS A 1357 |
| Chain | Residue |
| A | PHE227 |
| A | PRO228 |
| A | GLY229 |
| A | SER230 |
| B | LYS105 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS B 1356 |
| Chain | Residue |
| B | PHE227 |
| B | PRO228 |
| B | GLY229 |
| B | SER230 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 1358 |
| Chain | Residue |
| A | HIS188 |
| A | THR189 |
| A | LEU238 |
| A | ARG239 |
| A | TYR275 |
| A | HOH2105 |
| site_id | BC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 1357 |
| Chain | Residue |
| B | TYR121 |
| B | TRP122 |
| B | PHE185 |
| B | TRP187 |
| B | LEU244 |
| B | ILE245 |
| B | ALA277 |
| B | GLY278 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 1358 |
| Chain | Residue |
| B | GLY80 |
| B | SER246 |
| B | LEU248 |
| B | HOH2067 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 1359 |
| Chain | Residue |
| B | GLU235 |
| B | ALA236 |
| B | PHE237 |
| B | LEU238 |
| B | HOH2112 |
| B | HOH2132 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 1360 |
| Chain | Residue |
| A | HOH2062 |
| B | THR76 |
| B | LEU81 |
| B | PHE82 |
| B | THR83 |
| B | PHE227 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 1359 |
| Chain | Residue |
| A | GLY80 |
| A | PHE82 |
| A | TRP122 |
| A | SER246 |
| A | HOH2034 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1360 |
| Chain | Residue |
| A | GLU163 |
| B | LYS330 |
| B | HOH2152 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 1361 |
| Chain | Residue |
| A | PHE227 |
| A | SER230 |
| A | PHE237 |
| A | THR243 |
| A | HOH2116 |
| A | THR83 |
| site_id | CC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 1361 |
| Chain | Residue |
| B | ARG98 |
| B | ASN102 |
| site_id | CC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 1362 |
| Chain | Residue |
| B | TYR106 |
| B | ASN128 |
| B | PRO130 |
| B | TRP181 |
| B | LYS182 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 1363 |
| Chain | Residue |
| B | TYR18 |
| B | LYS46 |
| B | GLU263 |
| B | GLU266 |
| B | HOH2006 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 1362 |
| Chain | Residue |
| A | PHE114 |
| A | THR261 |
| A | GLU263 |
| A | HIS281 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 1363 |
| Chain | Residue |
| A | ASP158 |
| A | GLU161 |
| A | LYS162 |
| A | HOH2075 |
| site_id | CC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 1364 |
| Chain | Residue |
| A | GLU214 |
| A | HIS215 |
| site_id | CC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 1364 |
| Chain | Residue |
| B | PHE185 |
| B | HIS188 |
| B | LYS241 |
| B | PYR1355 |
| site_id | CC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1365 |
| Chain | Residue |
| A | TYR132 |
| A | PHE185 |
| A | PYR1356 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 1KA B 1365 |
| Chain | Residue |
| B | ALA12 |
| B | GLU214 |
| B | HIS215 |
| B | PRO256 |
| B | HOH2122 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16677698 |
| Chain | Residue | Details |
| A | TYR132 | |
| A | ASN198 | |
| A | LYS206 | |
| B | TYR132 | |
| B | ASN198 | |
| B | LYS206 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| 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 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
| Chain | Residue | Details |
| A | GLU190 | |
| B | GLU190 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| 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 | |
| A | HIS240 | |
| A | CYS306 | |
| A | CYS308 | |
| B | CYS234 | |
| B | HIS240 | |
| B | CYS306 | |
| B | CYS308 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:B2RXH2 |
| Chain | Residue | Details |
| A | LYS241 | |
| B | LYS241 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylalanine => ECO:0007744|PubMed:19413330 |
| Chain | Residue | Details |
| A | ALA2 | |
| B | 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 |
