2XJC
Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with guanosine monophosphate and diadenosine tetraphosphate
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 | 20 |
| Details | BINDING SITE FOR RESIDUE 5GP A 1489 |
| Chain | Residue |
| A | ASN52 |
| A | ASN250 |
| A | SER251 |
| A | LYS292 |
| A | GOL1498 |
| A | MG1499 |
| A | HOH2162 |
| A | HOH2305 |
| A | HOH2307 |
| A | HOH2366 |
| A | HOH2367 |
| A | MET53 |
| A | HOH2368 |
| A | ASP54 |
| A | PHE157 |
| A | ARG202 |
| A | ASP206 |
| A | HIS209 |
| A | LYS215 |
| A | THR249 |
| site_id | AC2 |
| Number of Residues | 36 |
| Details | BINDING SITE FOR RESIDUE B4P A 1490 |
| Chain | Residue |
| A | ARG144 |
| A | ARG144 |
| A | ASP145 |
| A | ASP145 |
| A | THR147 |
| A | ILE152 |
| A | ASN154 |
| A | ASN154 |
| A | PHE354 |
| A | PHE354 |
| A | LEU358 |
| A | LYS362 |
| A | LYS362 |
| A | GLN453 |
| A | GLN453 |
| A | ARG456 |
| A | ARG456 |
| A | TYR457 |
| A | TYR457 |
| A | GOL1494 |
| A | GOL1494 |
| A | HOH2370 |
| A | HOH2371 |
| A | HOH2371 |
| A | HOH2372 |
| A | HOH2372 |
| A | HOH2373 |
| A | HOH2373 |
| A | HOH2374 |
| A | HOH2374 |
| A | HOH2375 |
| A | HOH2376 |
| A | HOH2376 |
| A | HOH2377 |
| A | HOH2378 |
| A | HOH2378 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 1491 |
| Chain | Residue |
| A | PRO96 |
| A | THR97 |
| A | GLU374 |
| A | GLU378 |
| A | TYR434 |
| A | HOH2316 |
| A | HOH2379 |
| A | HOH2381 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 1492 |
| Chain | Residue |
| A | ARG39 |
| A | TYR115 |
| A | ASN117 |
| A | LYS361 |
| A | ARG367 |
| A | ASP459 |
| A | HOH2382 |
| A | HOH2383 |
| A | HOH2384 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 1493 |
| Chain | Residue |
| A | LEU57 |
| A | VAL227 |
| A | ASP229 |
| A | SER464 |
| A | PHE465 |
| A | ILE466 |
| A | HOH2346 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 1494 |
| Chain | Residue |
| A | ILE152 |
| A | ASN154 |
| A | HIS352 |
| A | B4P1490 |
| A | B4P1490 |
| A | HOH2386 |
| A | HOH2387 |
| A | HOH2389 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1495 |
| Chain | Residue |
| A | ASP257 |
| A | THR261 |
| A | PRO278 |
| A | GLN280 |
| A | HOH2390 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1496 |
| Chain | Residue |
| A | ASP252 |
| A | TYR253 |
| A | VAL288 |
| A | ASP289 |
| A | GLY310 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 1497 |
| Chain | Residue |
| A | ASP284 |
| A | GLN322 |
| A | HIS323 |
| A | GLY324 |
| A | ILE325 |
| A | HOH2291 |
| A | HOH2391 |
| A | HOH2392 |
| A | PHE283 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1498 |
| Chain | Residue |
| A | TYR210 |
| A | LYS215 |
| A | ASN250 |
| A | 5GP1489 |
| A | HOH2393 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 1499 |
| Chain | Residue |
| A | ASN52 |
| A | ASP54 |
| A | ASP351 |
| A | 5GP1489 |
| A | HOH2305 |
| A | HOH2307 |
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 |
