5L9V: Egl nine homolog 1

HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-1). Determined by X-ray diffraction at 1.83 Å resolution. Released 31 Aug 2016.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,864
Mol. weight: 60.06 kDa
Ligands: MN, OGA
Released: 31 Aug 2016

Explore 5L9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L9V contains 20 α-helices and 38 β-strands across 4 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, 17 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	236-237	2	1
β-strand	240	1	2
β-strand	252	1	3
β-strand	255-259	5	1
α-helix	267-283	17
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	393-402	10

Chain B: 8 helices, 17 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	5
α-helix	216-231	16
β-strand	236-237	2	5
β-strand	240	1	6
β-strand	252	1	7
β-strand	255-259	5	5
α-helix	267-283	17
β-strand	292-295	4	5
α-helix	296-297	2
β-strand	298-304	7	5
β-strand	308-313	6	7
β-strand	322-329	8	5
β-strand	331	1	8
α-helix	336-339	4
β-strand	340	1	7
β-strand	343-345	3	7
β-strand	354-356	3	7
β-strand	359	1	8
β-strand	362-367	6	5
β-strand	374-379	6	7
β-strand	382-392	11	5
α-helix	393-400	8

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	397-400	4
β-strand	402	1	2
α-helix	403	1
β-strand	409-410	2	1

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	397-399	3
β-strand	402	1	6
α-helix	403	1
β-strand	409-410	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Egl nine homolog 1	A, B	protein	252	Homo sapiens	Q9GZT9 (AlphaFold model)
Hypoxia-inducible factor 1-alpha	C, D	protein	19	Homo sapiens	Q16665 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5L9V_1 Egl nine homolog 1 (chains A, B)
GSHMASPNGQTKPLPALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGK
FTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLICHCNGKLGSYKING
RTKAMVACYPGNGTGYVRHVDNCNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFA
DIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKYLTGEKGVRVEL
NKPSDSVGKDVF

Sequence of entity 2 (C, D), FASTA

>5L9V_2 Hypoxia-inducible factor 1-alpha (chains C, D)
DACTLLAPAAGDTIISLCF

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
OGA	N-oxalylglycine	C4 H5 N O5	2

Primary citation

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases. Chowdhury, R., Leung, I.K., Tian, Y.M. et al. Nat Commun (2016) 7:12673-12673. DOI 10.1038/ncomms12673 · 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…

Browse structure collections

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