3HQU: PHD2:Fe:UN9:partial HIF1-alpha substrate complex

PHD2:Fe:UN9:partial HIF1-alpha substrate complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 28 Jul 2009.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,908
Mol. weight: 29.89 kDa
Ligands: FE2, UN9
Released: 28 Jul 2009

Explore 3HQU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HQU contains 8 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: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	190-193	4
α-helix	194-198	5
α-helix	199-205	7
β-strand	207-210	4	1
α-helix	216-231	16
β-strand	240-242	3	2
α-helix	247-249	3
β-strand	251-252	2	2
β-strand	255-259	5	1
α-helix	267-282	16
β-strand	292-295	4	1
β-strand	298-303	6	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	362-367	6	1
β-strand	374-379	6	3
β-strand	383-392	10	1
α-helix	393-398	6

Chain S: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	572	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Egl nine homolog 1	A	protein	246	Homo sapiens	Q9GZT9 (AlphaFold model)
Hypoxia-inducible factor 1 alpha	S	protein	17	Homo sapiens	Q16665 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3HQU_1 Egl nine homolog 1 (chains A)
PNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQL
VSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMV
ACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKF
DRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSDS
VGKDVF

Sequence of entity 2 (S), FASTA

>3HQU_2 Hypoxia-inducible factor 1 alpha (chains S)
DLEMLAPYIPMDDDFQL

Ligands and cofactors

ID	Name	Formula	Copies
FE2	FE (II) ion	Fe	1
UN9	N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine	C12 H9 Cl N2 O4	1

Primary citation

Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases. Chowdhury, R., McDonough, M.A., Mecinovic, J. et al. Structure (2009) 17:981-989. DOI 10.1016/j.str.2009.06.002 · 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…
6YW1 1.46 Å, HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent…
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…

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