9DKC: URAT1

Structure of URAT1 in complex with TD-3. Determined by electron microscopy at 2.55 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,847
Mol. weight: 55.84 kDa
Ligands: A1A45
Released: 18 Jun 2025

Explore 9DKC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DKC contains 36 α-helices and 6 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: 36 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	15-36	22
α-helix	38-41	4
β-strand	48-49	2	1
α-helix	50	1
α-helix	52-55	4
α-helix	57-62	6
α-helix	69-74	6
β-strand	79-80	2	2
β-strand	84-85	2	2
β-strand	90-91	2	3
α-helix	96-99	4
α-helix	110-112	3
β-strand	113-114	2	3
β-strand	120-121	2	1
α-helix	131-135	5
α-helix	139-141	3
α-helix	144-167	24
α-helix	173-190	18
α-helix	196-224	29
α-helix	227-229	3
α-helix	230-252	23
α-helix	259-266	8
α-helix	268-275	8
α-helix	280-282	3
α-helix	283-288	6
α-helix	293-306	14
α-helix	309-314	6
α-helix	317-323	7
α-helix	325-329	5
α-helix	333-335	3
α-helix	337-339	3
α-helix	344-346	3
α-helix	347-369	23
α-helix	371-374	4
α-helix	378-402	25
α-helix	405-425	21
α-helix	431-459	29
α-helix	465-485	21
α-helix	486-491	6
α-helix	495-511	17
α-helix	516-517	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
URAT1	A	protein	518	Homo sapiens	Q96S37 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DKC_1 URAT1 (chains A)
MAFSELLDQVGGLGRFQVLQTVALVVPIMWLCTQSMLENFSAAVPSHRCWVPLLDNSTAQ
ASVPGALGPEALLAVSIPPGPNQGPHQCRRFRQPQWQLLDPNATATNWSEAATEPCVDGW
VYDRSTFTSTIVAKWDLVCDSQALKPMAQSIYLAGILVGAAVCGPASDRFGRRLVLTWSY
LQMAVSGTAAAFAPTFPVYCLFRFLVAFAVAGVMMNTGTLVMEWTSAQARPLVMTLNSLG
FSFGHVLMAAVAYGVRDWALLQLVVSVPFFLCFVYSCWLAESARWLLITGRLDRGLRELQ
RVAAINGKRAVGDTLTPQVLLSAMQEELSVGQAPASLGTLLRTPGLRLRTCISTLCWFAF
GFTFFGLALDLQALGSNIFLLQVLIGVVDIPAKIGTLLLLSRLGRRPTQAASLVLAGLCI
LANTLVPHEMGALRSALAVLGLGGLGAAFTCITIYSGELFPTVLRMTAVGLGQMAARGGA
ILGPLVRLLGVHGPWLPLLVYGTVPVLSGLAALLLPET

Ligands and cofactors

ID	Name	Formula	Copies
A1A45	2-({1-[(4-bromonaphthalen-1-yl)methyl]-1H-imidazo[4,5-b]pyridin-2-yl}sulfanyl)-…	C21 H18 Br N3 O2 S	1

Primary citation

Molecular basis of the urate transporter URAT1 inhibition by gout drugs. Suo, Y., Fedor, J.G., Zhang, H. et al. Nat Commun (2025) 16:5178-5178. DOI 10.1038/s41467-025-60480-3 · PubMed

Other PDB entries of the same protein (UniProt Q96S37 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RXO 1.2 Å, Structure of the PDZ2 domain from human PDZK1 (NHERF3) with the C-terminal residues…
9RXR 1.69 Å, Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues…
9RXS 2.0 Å, Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues…
9DK9 2.68 Å, Structure of URAT1 with no external ligand added
9B1G 2.7 Å, Human urate transporter 1 URAT1 in complex with dotinurad
9DKB 2.74 Å, Structure of URAT1 in complex with lesinurad
9B1F 2.9 Å, Human urate transporter 1 URAT1 in apo state
9B1H 2.9 Å, Human urate transporter 1 URAT1 in complex with lesinurad
8WJG 3.0 Å, Cryo-EM structure of URAT1(R477S)
9B1J 3.0 Å, Urate bound human URAT1 in the inward-facing state
9B1M 3.0 Å, Pyrazinoate bound human URAT1 in the inward-facing state (site1)
9DKA 3.0 Å, Structure of URAT1 in complex with benzbromarone

Browse structure collections

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