6YW1: HIF prolyl hydroxylase 2

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent allosteric cyclic peptide 3C (14-mer). Determined by X-ray diffraction at 1.46 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 1.46 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,121
Mol. weight: 28.1 kDa
Ligands: BCT, AKG, MN
Released: 30 Dec 2020

Explore 6YW1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YW1 contains 9 α-helices and 17 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.

Chain A: 9 helices, 16 β-strands

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	252	1	2
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	2
β-strand	322-329	8	1
β-strand	331	1	3
α-helix	336-339	4
β-strand	340	1	2
β-strand	343-345	3	2
β-strand	354-356	3	2
β-strand	359	1	3
β-strand	362-367	6	1
β-strand	374-379	6	2
β-strand	382-392	11	1
α-helix	393-397	5

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9-11	3	1

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>6YW1_1 Egl nine homolog 1 (chains A)
GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGK
FTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKING
RTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFA
DIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE

Sequence of entity 2 (B), FASTA

>6YW1_2 PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER) (chains B)
XYVWLTDTWVLSRT

Ligands and cofactors

ID	Name	Formula	Copies
BCT	Bicarbonate ion	C H O3	1
AKG	2-oxoglutaric acid	C5 H6 O5	1
MN	Manganese (II) ion	Mn	1

Primary citation

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:

7Q5V 1.17 Å, Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with N-oxalylglycine (NOG) and hif-2…
7Q5X 1.21 Å, Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 2-oxoglutarate (2OG) and hif-2…
8Q64 1.36 Å, Crystal structure of hydroxylated HIF2alpha-CODD peptide (523-542) bound to apo-HIF…
8Q6E 1.37 Å, Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with…
8RV1 1.39 Å, HIF prolyl hydroxylase 2 (PHD2) T387S variant bound to acetate (ACT) and hydroxylated…
6QGV 1.4 Å, HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with a Spiro[4.5]decanone inhibitor…
8Q6D 1.4 Å, Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with…
8Q5S 1.49 Å, Anaerobic crystal structure of apo-HIF prolyl hydroxylase 2 (PHD2 181-407)in complex…
6YW4 1.53 Å, HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a…
4BQY 1.53 Å, HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Fe(II) and…
6NMQ 1.58 Å, Hypoxia-Inducible Factor (HIF) Prolyl Hydroxylase 2 (PHD2) in Complex with the…
2HBT 1.6 Å, Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active…

Browse structure collections

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