5APH: Ligand complex of RORg LBD

Ligand complex of RORg LBD. Determined by X-ray diffraction at 1.54 Å resolution. Released 25 Nov 2015.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,509
Mol. weight: 32.89 kDa
Ligands: VYI
Released: 25 Nov 2015

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

Secondary structure: helices and β-sheets

5APH contains 19 α-helices and 4 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: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	267-282	16
α-helix	289-294	6
α-helix	295-297	3
β-strand	299	1	1
α-helix	302-310	9
α-helix	313-337	25
α-helix	341-343	3
α-helix	346-364	19
α-helix	365-368	4
β-strand	369-370	2	1
β-strand	375-378	4	1
β-strand	381-383	3	1
α-helix	385-391	7
α-helix	394-408	15
α-helix	414-425	12
α-helix	436-456	21
α-helix	460-465	6
α-helix	467-468	2
α-helix	469-489	21
α-helix	491-497	7
α-helix	500-506	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	690-695	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear receptor ror-gamma	A	protein	266	HOMO SAPIENS	P51449 (AlphaFold model)
Nuclear receptor coactivator 2	C	protein	12	HOMO SAPIENS	Q15596 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5APH_1 NUCLEAR RECEPTOR ROR-GAMMA (chains A)
HNHNHNHNHNHNGGENLYFQGASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSRE
EVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLV
RMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTAL
VLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERL
QIFQHLHPIVVQAAFPPLYKELFSGG

Sequence of entity 2 (C), FASTA

>5APH_2 NUCLEAR RECEPTOR COACTIVATOR 2 (chains C)
KHKILHRLLQDS

Ligands and cofactors

ID	Name	Formula	Copies
VYI	N-(2-fluorophenyl)-4-[(4-fluorophenyl)sulfonyl]-2,3,4,5-tetrahydro-1,4-benzoxaz…	C21 H18 F2 N2 O3 S	1

Water and common crystallization additives (DMS) are not listed.

Primary citation

Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor ROR gamma. Olsson, R.I., Xue, Y., von Berg, S. et al. ChemMedChem (2016) 11:207-216. DOI 10.1002/cmdc.201500432 · PubMed

Other PDB entries of the same protein (UniProt P51449 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NPC 1.47 Å, ROR(gamma)t ligand binding domain in complex with allosteric ligand FM156
6T4X 1.48 Å, ROR(gamma)t ligand binding domain in complex with 25-hydroxycholesterol and allosteric…
6R7K 1.54 Å, Ligand complex of RORg LBD
7NP5 1.55 Å, ROR(gamma)t ligand binding domain in complex with allosteric ligand FM216
6W9I 1.61 Å, Substituted benzyloxytricyclic compounds as retinoic acid-related orphan receptor gamma…
6SAL 1.61 Å, ROR(gamma)t ligand binding domain in complex with allosteric ligand FM26
7OFK 1.61 Å, Ligand complex of RORg LBD
6T4T 1.62 Å, ROR(gamma)t ligand binding domain in complex with 20-alpha-hydroxycholesterol and…
7KXD 1.62 Å, Crystal structure of rar-related orphan receptor C (nhis-RORGT(244-487)-L6-SRC1(678-692))…
9N9L 1.64 Å, An RORgt Inverse agonist for treatment of Psoriasis
5NTW 1.64 Å, Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding…
6G07 1.66 Å, Rorgt (264-518;C455S) in complex with inverse agonist "cpd-9" and RIP140 peptide at 1.66A

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