5JWP: Human FIH D201E variant

Crystal structure of human FIH D201E variant in complex with Zn, alpha-ketoglutarate, and HIF1 alpha peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 23 Nov 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,114
Mol. weight: 43.33 kDa
Ligands: AKG, ZN
Released: 23 Nov 2016

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

Secondary structure: helices and β-sheets

5JWP contains 21 α-helices and 21 β-strands across 1 chain. 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: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	16-17	2
β-strand	18	1	1
α-helix	19	1
β-strand	25	1	1
α-helix	29-31	3
β-strand	39-41	3	2
α-helix	42-43	2
β-strand	44-45	2	3
α-helix	50-57	8
β-strand	62-64	3	3
α-helix	71-75	5
α-helix	78-84	7
β-strand	90-95	6	3
β-strand	99	1	2
α-helix	105-107	3
β-strand	118-123	6	3
α-helix	125-137	13
β-strand	143-149	7	3
α-helix	156-163	8
α-helix	167-177	11
β-strand	182-184	3	3
β-strand	186-190	5	3
β-strand	195-199	5	2
β-strand	204-211	8	3
β-strand	214-219	6	2
α-helix	221-223	3
α-helix	224-227	4
β-strand	229	1	4
α-helix	230-231	2
β-strand	239	1	2
β-strand	240	1	4
α-helix	253-257	5
β-strand	260-265	6	2
β-strand	270-273	4	3
β-strand	278-283	6	2
α-helix	284	1
β-strand	290-297	8	3
α-helix	298-303	6
α-helix	310-311	2
α-helix	312-330	19
α-helix	333-335	3
α-helix	336-344	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hypoxia-inducible factor 1-alpha inhibitor	A	protein	352	Homo sapiens	Q9NWT6 (AlphaFold model)
Hypoxia-inducible factor 1-alpha	B	protein	19	Homo sapiens	Q16665 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JWP_1 Hypoxia-inducible factor 1-alpha inhibitor (chains A)
GSHMAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIE
NEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPR
SNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKR
GWGQLTSNLLLIGMEGNVTPAHYEEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCD
RQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWY
KGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN

Sequence of entity 2 (B), FASTA

>5JWP_2 Hypoxia-inducible factor 1-alpha (chains B)
DESGLPQLTSYDAEVNAPI

Ligands and cofactors

ID	Name	Formula	Copies
AKG	2-oxoglutaric acid	C5 H6 O5	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

The facial triad in the alpha-ketoglutarate dependent oxygenase FIH: A role for sterics in linking substrate binding to O2 activation. Hangasky, J.A., Taabazuing, C.Y., Martin, C.B. et al. J Inorg Biochem (2016) 166:26-33. DOI 10.1016/j.jinorgbio.2016.10.007 · PubMed

Other PDB entries of the same protein (UniProt Q9NWT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7A1Q 1.75 Å, FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II), 3-(carboxycarbonyl)cyclopentane-1-c…
7A1P 1.76 Å, FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II), 4-propyl-2-oxoglutarate, AND…
6H9J 1.83 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (229-255)
6HC8 1.9 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPA1 (313-339)
6HKP 1.9 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP2 (970-992)
7A1J 1.9 Å, FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-(3-phenylpropyl)-2-oxoglutarate
6HL6 1.97 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and iASPP(670-693)
6HA6 1.98 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (220-246)
6HL5 1.98 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP1(932-954)
7A1K 1.99 Å, FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND…
7A1N 2.01 Å, FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II), 3-methyl-2-oxoglutarate, AND…
7A1S 2.01 Å, FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II), 3-methyl-2-oxoglutarate, AND…

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