HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA CODD (556-574) and a RaPID-derived cyclic peptide 3C (14-mer). Determined by X-ray diffraction at 2.28 Å resolution. Released 30 Dec 2020.
Explore 6YW3 in 3D Show helices and sheets RCSB PDB PDBe
6YW3 contains 12 α-helices and 20 β-strands across 3 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 |
|---|---|---|---|
| α-helix | 187-189 | 3 | |
| α-helix | 190-193 | 4 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-205 | 7 | |
| β-strand | 207-211 | 5 | 1 |
| α-helix | 216-231 | 16 | |
| β-strand | 236-237 | 2 | 1 |
| β-strand | 240 | 1 | 2 |
| α-helix | 248-250 | 3 | |
| β-strand | 252 | 1 | 3 |
| β-strand | 255-259 | 5 | 1 |
| α-helix | 267-282 | 16 | |
| β-strand | 292-295 | 4 | 1 |
| α-helix | 296-297 | 2 | |
| β-strand | 298-304 | 7 | 1 |
| β-strand | 308-313 | 6 | 3 |
| β-strand | 322-329 | 8 | 1 |
| β-strand | 331 | 1 | 4 |
| α-helix | 336-339 | 4 | |
| β-strand | 340 | 1 | 3 |
| β-strand | 343-345 | 3 | 3 |
| β-strand | 354-356 | 3 | 3 |
| β-strand | 359 | 1 | 4 |
| β-strand | 363-367 | 5 | 1 |
| β-strand | 374-379 | 6 | 3 |
| β-strand | 382-392 | 11 | 1 |
| α-helix | 393-399 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 9-11 | 3 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 560-562 | 3 | |
| β-strand | 564 | 1 | 2 |
| α-helix | 565 | 1 | |
| β-strand | 572-573 | 2 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Egl nine homolog 1 | A | protein | 233 | Homo sapiens | Q9GZT9 (AlphaFold model) |
| PHD2-specific rapid cyclic peptide 3C (14-mer) | B | protein | 14 | synthetic construct | |
| Hypoxia-inducible factor 1-alpha | S | protein | 19 | Homo sapiens | Q16665 (AlphaFold model) |
>6YW3_1 Egl nine homolog 1 (chains A) GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGK FTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKING RTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFA DIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
>6YW3_2 PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER) (chains B) XYVWLTDTWVLSRT
>6YW3_3 Hypoxia-inducible factor 1-alpha (chains S) DLDLEMLAPYIPMDDDFQL
Water and common crystallization additives (SO4, GOL) are not listed.
Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2. Chowdhury, R., Abboud, M.I., McAllister, T.E. et al. Sci Rep (2020) 10:21964-21964. DOI 10.1038/s41598-020-76307-8 · PubMed
Other PDB entries of the same protein (UniProt Q9GZT9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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