5NTN: Nuclear receptor ROR-gamma

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,068
Mol. weight: 130.05 kDa
Ligands: 98H
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5NTN contains 68 α-helices and 16 β-strands across 8 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: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	267-284	18
α-helix	289-294	6
α-helix	295-297	3
β-strand	299	1	1
α-helix	302-309	8
α-helix	313-337	25
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 B: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	267-284	18
α-helix	289-294	6
β-strand	299	1	2
α-helix	302-309	8
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	2
β-strand	375-378	4	2
β-strand	381-383	3	2
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: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	267-284	18
α-helix	289-294	6
β-strand	299	1	3
α-helix	302-310	9
α-helix	313-336	24
α-helix	346-364	19
α-helix	365-368	4
β-strand	369-370	2	3
β-strand	375-378	4	3
β-strand	381-383	3	3
α-helix	385-391	7
α-helix	394-408	15
α-helix	414-425	12
α-helix	436-455	20
α-helix	460-463	4
α-helix	467-468	2
α-helix	469-489	21
α-helix	491-497	7
α-helix	500-506	7

Chain D: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	267-284	18
α-helix	289-294	6
α-helix	295-297	3
β-strand	299	1	4
α-helix	302-310	9
α-helix	313-337	25
α-helix	339-342	4
α-helix	346-364	19
α-helix	365-368	4
β-strand	369-370	2	4
β-strand	375-378	4	4
β-strand	381-383	3	4
α-helix	385-391	7
α-helix	394-408	15
α-helix	414-425	12
α-helix	436-455	20
α-helix	460-463	4
α-helix	467-468	2
α-helix	469-489	21
α-helix	491-497	7
α-helix	500-506	7

Chains P, Q and S: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	500-505	6

Chain R: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	500-504	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear receptor ROR-gamma	A, B, C, D	protein	257	Homo sapiens	P51449 (AlphaFold model)
Nuclear receptor-interacting protein 1	P, Q, R, S	protein	20	Homo sapiens	P48552 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5NTN_1 Nuclear receptor ROR-gamma (chains A, B, C, D)
GPYASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCA
HHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGK
YGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQ
LQYNLELAFHHHLSKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPL
YKELFSTETESPVGLSK

Sequence of entity 2 (P, Q, R, S), FASTA

>5NTN_2 Nuclear receptor-interacting protein 1 (chains P, Q, R, S)
NSHQKVTLLQLLLGHKNEEN

Ligands and cofactors

ID	Name	Formula	Copies
98H	(5R,10S,13R,14R,17R)-17-((R,E)-7-hydroxy-6-methylhept-5-en-2-yl)-4,4,10,13,14-p…	C30 H46 O3	4

Primary citation

Structural States of ROR gamma t: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds. Kallen, J., Izaac, A., Be, C. et al. ChemMedChem (2017) 12:1014-1021. DOI 10.1002/cmdc.201700278 · 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…
5APH 1.54 Å, Ligand complex of RORg LBD
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…

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