MolNFT v1 · #124052 · protein

Crystal structure of retinoic acid receptor-related orphan receptor (ror) gamma ligand binding domain complex with 444

5K3L · Nuclear receptor ror-gamma: “Crystal structure of retinoic acid receptor-related orphan receptor (ror) gamma ligand binding domain complex…”. X-ray diffraction, 1 ligand (444), 20 pockets (best druggability 0.84). MolNFT v1 #124052…

PDB: 5K3L
Type: protein
Length: 903 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor ror-gamma
UniProt: P51449
Ligands: 444
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor ror-gamma	protein	225	65% helix, 4% strand	P51449
B, C, D	Nuclear receptor ror-gamma	protein	226	67% helix, 5% strand	P51449

Ligands and binding sites

444 · N-(2,2,2-trifluoroethyl)-N-{4-[2,2,2-trifluoro-1-hydroxy-1-(trifluoromethyl) ethyl]phenyl}benzenesulfonamide · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.84	0.89	40	444
2	433	0.84	0.91	36	444
3	537	0.84	0.89	36	444
4	426	0.83	0.91	41	444
5	571	0.71	0.79	57	empty

Interfaces

5 interfaces between chains.

C–D · 866 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 793 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 687 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 181 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 126 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5K3L · Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand… · the same entry in another collection · chain C against C, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P51449
Elsewhere: RCSB PDB 5K3L · PDBe 5K3L · UniProt P51449

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