6D09: PT2440

Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex. Determined by X-ray diffraction at 1.85 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,846
Mol. weight: 28.19 kDa
Ligands: FOJ
Released: 31 Oct 2018

Explore 6D09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D09 contains 13 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	240-242	3
β-strand	243-248	6	1
β-strand	253	1	2
β-strand	254-257	4	1
α-helix	260-265	6
α-helix	269-272	4
β-strand	276	1	2
α-helix	277-280	4
β-strand	281	1	1
α-helix	283-285	3
α-helix	286-299	14
β-strand	301-303	3	1
β-strand	307-310	4	1
β-strand	316-326	11	1
β-strand	336-343	8	1

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	359-361	3
β-strand	362-367	6	3
β-strand	372	1	4
β-strand	373-376	4	3
α-helix	380-384	5
α-helix	388-391	4
β-strand	395	1	4
α-helix	396-399	4
β-strand	400	1	3
α-helix	402-404	3
α-helix	405-415	11
β-strand	423-430	8	3
β-strand	436-446	11	3
α-helix	453-455	3
β-strand	456-463	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endothelial PAS domain-containing protein 1	A	protein	117	Homo sapiens	Q99814 (AlphaFold model)
Aryl hydrocarbon receptor nuclear translocator	B	protein	121	Homo sapiens	P27540 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6D09_1 Endothelial PAS domain-containing protein 1 (chains A)
GEFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSH
QNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN

Sequence of entity 2 (B), FASTA

>6D09_2 Aryl hydrocarbon receptor nuclear translocator (chains B)
GEFKGLNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLR
DSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQ
E

Ligands and cofactors

ID	Name	Formula	Copies
FOJ	3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-b…	C16 H8 F5 N O4 S	1

Primary citation

Crystal structure of PT1940 bound to HIF2a-B*:ARNT-B* complex. Du, X. To be published.

Other PDB entries of the same protein (UniProt Q99814 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F1P 1.17 Å, Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
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…
8Q6D 1.4 Å, Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with…
3F1N 1.48 Å, Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
8Q5S 1.49 Å, Anaerobic crystal structure of apo-HIF prolyl hydroxylase 2 (PHD2 181-407)in complex…
3H82 1.5 Å, Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
4GHI 1.5 Å, Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
6D0C 1.5 Å, Crystal structure of HIF2a-B*:ARNT-B* complex

Browse structure collections

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