2XJD
Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inorganic phosphate and deoxyadenosine triphosphate
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000255 | biological_process | allantoin metabolic process |
A | 0005515 | molecular_function | protein binding |
A | 0005524 | molecular_function | ATP binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0006204 | biological_process | IMP catabolic process |
A | 0008253 | molecular_function | 5'-nucleotidase activity |
A | 0009117 | biological_process | nucleotide metabolic process |
A | 0016740 | molecular_function | transferase activity |
A | 0016787 | molecular_function | hydrolase activity |
A | 0042802 | molecular_function | identical protein binding |
A | 0046037 | biological_process | GMP metabolic process |
A | 0046040 | biological_process | IMP metabolic process |
A | 0046054 | biological_process | dGMP metabolic process |
A | 0046085 | biological_process | adenosine metabolic process |
A | 0046872 | molecular_function | metal ion binding |
A | 0050146 | molecular_function | nucleoside phosphotransferase activity |
A | 0050483 | molecular_function | IMP 5'-nucleotidase activity |
A | 0050484 | molecular_function | GMP 5'-nucleotidase activity |
A | 0050689 | biological_process | negative regulation of defense response to virus by host |
A | 0061630 | molecular_function | ubiquitin protein ligase activity |
A | 0070936 | biological_process | protein K48-linked ubiquitination |
A | 0106411 | molecular_function | XMP 5'-nucleosidase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE ATP A 1489 |
Chain | Residue |
A | ARG144 |
A | MG1498 |
A | MG1498 |
A | HOH2175 |
A | HOH2176 |
A | HOH2381 |
A | HOH2382 |
A | HOH2438 |
A | HOH2439 |
A | HOH2440 |
A | HOH2441 |
A | ASP145 |
A | HOH2442 |
A | HOH2443 |
A | HOH2444 |
A | ASN154 |
A | PHE354 |
A | LYS362 |
A | GLN453 |
A | ARG456 |
A | ARG456 |
A | TYR457 |
site_id | AC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL A 1490 |
Chain | Residue |
A | HIS209 |
A | TYR210 |
A | LYS215 |
A | SER251 |
A | TYR255 |
A | GOL1493 |
A | HOH2445 |
site_id | AC3 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE GOL A 1491 |
Chain | Residue |
A | PHE283 |
A | ASP284 |
A | ILE286 |
A | LEU321 |
A | GLN322 |
A | HIS323 |
A | GLY324 |
A | ILE325 |
A | HOH2353 |
A | HOH2446 |
A | HOH2447 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL A 1492 |
Chain | Residue |
A | PHE198 |
A | GLN199 |
A | ARG202 |
A | HOH2188 |
A | HOH2231 |
A | HOH2449 |
site_id | AC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL A 1493 |
Chain | Residue |
A | PHE157 |
A | ARG202 |
A | VAL205 |
A | ASP206 |
A | TYR210 |
A | GOL1490 |
site_id | AC6 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL A 1494 |
Chain | Residue |
A | PRO96 |
A | GLU374 |
A | GLU378 |
A | TYR434 |
A | HOH2391 |
A | HOH2451 |
A | HOH2453 |
A | HOH2454 |
A | HOH2455 |
site_id | AC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL A 1495 |
Chain | Residue |
A | ASP257 |
A | THR261 |
A | PRO278 |
A | TRP279 |
A | GLN280 |
A | HOH2456 |
A | HOH2457 |
site_id | AC8 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE PO4 A 1496 |
Chain | Residue |
A | ASN52 |
A | MET53 |
A | ASP54 |
A | THR249 |
A | ASN250 |
A | SER251 |
A | LYS292 |
A | MG1497 |
A | HOH2372 |
A | HOH2374 |
A | HOH2445 |
A | HOH2458 |
site_id | AC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A 1497 |
Chain | Residue |
A | ASN52 |
A | ASP54 |
A | ASP351 |
A | PO41496 |
A | HOH2372 |
A | HOH2374 |
site_id | BC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 1498 |
Chain | Residue |
A | LYS362 |
A | ATP1489 |
A | ATP1489 |
A | HOH2381 |
A | HOH2381 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 1 |
Details | ACT_SITE: Nucleophile => ECO:0000305|PubMed:21396942 |
Chain | Residue | Details |
A | ASN52 |
site_id | SWS_FT_FI2 |
Number of Residues | 1 |
Details | ACT_SITE: Proton donor => ECO:0000305|PubMed:21396942 |
Chain | Residue | Details |
A | ASP54 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:17405878, ECO:0000269|PubMed:21396942, ECO:0007744|PDB:2J2C, ECO:0007744|PDB:2JC9, ECO:0007744|PDB:2JCM, ECO:0007744|PDB:2XCV, ECO:0007744|PDB:2XCW, ECO:0007744|PDB:2XJB, ECO:0007744|PDB:2XJC, ECO:0007744|PDB:2XJD, ECO:0007744|PDB:2XJE |
Chain | Residue | Details |
A | ASN52 | |
A | ASP54 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:21396942, ECO:0007744|PDB:2XJB |
Chain | Residue | Details |
A | ARG144 | |
A | ARG456 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:21396942, ECO:0007744|PDB:2XJC |
Chain | Residue | Details |
A | ASN154 | |
A | LYS362 | |
A | GLN453 | |
A | TYR457 |
site_id | SWS_FT_FI6 |
Number of Residues | 7 |
Details | BINDING: BINDING => ECO:0000269|PubMed:21396942, ECO:0007744|PDB:2XCV, ECO:0007744|PDB:2XCW |
Chain | Residue | Details |
A | ARG202 | |
A | ASP206 | |
A | LYS215 | |
A | THR249 | |
A | ASN250 | |
A | SER251 | |
A | LYS292 |
site_id | SWS_FT_FI7 |
Number of Residues | 1 |
Details | BINDING: BINDING => ECO:0000269|PubMed:17405878, ECO:0000269|PubMed:21396942, ECO:0007744|PDB:2J2C, ECO:0007744|PDB:2JC9, ECO:0007744|PDB:2JCM |
Chain | Residue | Details |
A | ASP351 |
site_id | SWS_FT_FI8 |
Number of Residues | 1 |
Details | BINDING: BINDING => ECO:0000269|PubMed:17405878, ECO:0007744|PDB:2JC9 |
Chain | Residue | Details |
A | MET436 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
A | SER418 | |
A | SER511 |
site_id | SWS_FT_FI10 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648 |
Chain | Residue | Details |
A | SER502 |
site_id | SWS_FT_FI11 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q3V1L4 |
Chain | Residue | Details |
A | SER527 |