Crystal structure of PTPRD phosphatase domain in complex with Liprin-alpha3 tandem SAM domains. Determined by X-ray diffraction at 1.91 Å resolution. Released 12 Feb 2020.
Explore 6KIP in 3D Show helices and sheets RCSB PDB PDBe
6KIP contains 40 α-helices and 19 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 1216-1217 | 2 | 1 |
| α-helix | 1218-1220 | 3 | |
| α-helix | 1221-1229 | 9 | |
| α-helix | 1239-1246 | 8 | |
| α-helix | 1259-1261 | 3 | |
| α-helix | 1263-1268 | 6 | |
| α-helix | 1278-1280 | 3 | |
| β-strand | 1281 | 1 | 2 |
| α-helix | 1283-1286 | 4 | |
| β-strand | 1287 | 1 | 3 |
| β-strand | 1290 | 1 | 3 |
| β-strand | 1298-1301 | 4 | 2 |
| β-strand | 1310-1314 | 5 | 2 |
| α-helix | 1315-1317 | 3 | |
| α-helix | 1318-1320 | 3 | |
| α-helix | 1321-1330 | 10 | |
| β-strand | 1335-1338 | 4 | 2 |
| β-strand | 1343-1344 | 2 | 4 |
| β-strand | 1347-1348 | 2 | 4 |
| β-strand | 1360-1362 | 3 | 2 |
| β-strand | 1365-1375 | 11 | 2 |
| β-strand | 1378-1387 | 10 | 2 |
| β-strand | 1393-1401 | 9 | 2 |
| α-helix | 1414-1429 | 16 | |
| α-helix | 1435 | 1 | |
| β-strand | 1436-1440 | 5 | 2 |
| α-helix | 1446-1463 | 18 | |
| β-strand | 1465-1466 | 2 | 1 |
| α-helix | 1468-1476 | 9 | |
| α-helix | 1486-1500 | 15 | |
| β-strand | 1503 | 1 | 5 |
| α-helix | 1504-1506 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 812 | 1 | 5 |
| α-helix | 813-830 | 18 | |
| α-helix | 835-837 | 3 | |
| β-strand | 839 | 1 | 6 |
| α-helix | 840-846 | 7 | |
| α-helix | 847-851 | 5 | |
| α-helix | 855-864 | 10 | |
| β-strand | 867 | 1 | 6 |
| α-helix | 868-872 | 5 | |
| α-helix | 876-882 | 7 | |
| α-helix | 888-904 | 17 | |
| α-helix | 954-956 | 3 | |
| α-helix | 957-961 | 5 | |
| α-helix | 962-964 | 3 | |
| α-helix | 968-970 | 3 | |
| α-helix | 971-976 | 6 | |
| α-helix | 981-984 | 4 | |
| α-helix | 989-993 | 5 | |
| α-helix | 1001-1016 | 16 | |
| α-helix | 1021-1029 | 9 | |
| α-helix | 1038-1040 | 3 | |
| α-helix | 1043-1052 | 10 | |
| α-helix | 1056-1059 | 4 | |
| α-helix | 1060-1062 | 3 | |
| α-helix | 1069-1074 | 6 | |
| α-helix | 1080-1086 | 7 | |
| α-helix | 1094-1111 | 18 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Receptor-type tyrosine-protein phosphatase delta | A | protein | 305 | Mus musculus | Q64487 (AlphaFold model) |
| Liprin-alpha-3 | B | protein | 331 | Mus musculus | P60469 (AlphaFold model) |
>6KIP_1 Receptor-type tyrosine-protein phosphatase delta (chains A) MNTEVPARNLYAYIQKLTQIETGENVTGMELEFKRLASSKAHTSRFISANLPCNKFKNRL VNIMPYESTRVCLQPIRGVEGSDYINASFLDGYRQQKAYIATQGPLAETTEDFWRMLWEH NSTIVVMLTKLREMGREKCHQYWPAERSARYQYFVVDPMAEYNMPQYILREFKVTDARDG QSRTVRQFQFTDWPEQGVPKSGEGFIDFIGQVHKTKEQFGQDGPISVHCSAGVGRTGVFI TLSIVLERMRYEGVVDIFQTVKMLRTQRPAMVQTEDQYQFCYRAALEYLGSFDHYATLEH HHHHH
>6KIP_2 Liprin-alpha-3 (chains B) LGSAKLTGPGDKDRRNKRKHELLEEACRQGLPFAAWDGPTVVSWLELWVGMPAWYVAACR ANVKSGAIMANLSDTEIQREIGISNPLHRLKLRLAIQEMVSLTSPSAPASSRTPTGNVWM THEEMESLTAATKPETKEISWEQILAYGDMNHEWVGNDWLPSLGLPQYRSYFMESLVDAR MLDHLNKKELRGQLKMVDSFHRVSLHYGIMCLKRLNYDRKDLERRREESQTQIRDVMVWS NERVMGWVSGLGLKEFATNLTESGVHGALLALDETFDYSDLALLLQIPTQNAQARQLLEK EFSNLISLGTDRRLDEDSAKSFSRSTRAAAS
Structural insights into selective interaction between type IIa receptor protein tyrosine phosphatases and Liprin-alpha. Wakita, M., Yamagata, A., Shiroshima, T. et al. Nat Commun (2020) 11:649-649. DOI 10.1038/s41467-020-14516-5 · PubMed
Other PDB entries of the same protein (UniProt Q64487 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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