9R8Y: Carbonic anhydrase 9

Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide. Determined by X-ray diffraction at 1.95 Å resolution. Released 8 Oct 2025.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,172
Mol. weight: 114.1 kDa
Ligands: ZN, A1JDL
Released: 8 Oct 2025

Explore 9R8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9R8Y contains 45 α-helices and 88 β-strands across 4 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	32-33	2	1
α-helix	35-37	3
β-strand	39-40	2	2
α-helix	45-47	3
β-strand	48-50	3	2
β-strand	53	1	3
β-strand	60-64	5	2
β-strand	69-72	4	2
β-strand	78-82	5	2
β-strand	85-96	12	2
β-strand	98	1	4
β-strand	101	1	4
β-strand	107-108	2	1
β-strand	111	1	1
α-helix	112-113	2
β-strand	115-123	9	2
α-helix	129-132	4
β-strand	139-149	11	2
α-helix	152-153	2
α-helix	154-160	7
α-helix	164-166	3
β-strand	172-175	4	2
β-strand	179	1	3
α-helix	180-183	4
β-strand	191-197	7	2
β-strand	205-212	8	2
β-strand	216-219	4	2
α-helix	220-226	7
β-strand	231	1	5
β-strand	237	1	5
α-helix	243-245	3
β-strand	254-255	2	2

Chain B: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	32-33	2	6
α-helix	35-37	3
α-helix	38	1
β-strand	39-40	2	7
α-helix	45-47	3
β-strand	48-50	3	7
β-strand	53	1	8
β-strand	60-64	5	7
β-strand	69-72	4	7
α-helix	73-74	2
β-strand	78-82	5	7
β-strand	85-96	12	7
β-strand	98	1	9
β-strand	101	1	9
β-strand	107-108	2	6
β-strand	111-112	2	6
α-helix	113	1
β-strand	115-123	9	7
α-helix	129-132	4
β-strand	139-148	10	7
α-helix	154-160	7
α-helix	163-166	4
β-strand	172-175	4	7
β-strand	179	1	8
α-helix	180-183	4
β-strand	191-197	7	7
β-strand	205-212	8	7
β-strand	216-218	3	7
α-helix	220-228	9
β-strand	231	1	10
β-strand	237	1	10
α-helix	243-245	3
β-strand	254-255	2	7

Chain C: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	32-33	2	11
α-helix	35-37	3
α-helix	38	1
β-strand	39-40	2	12
α-helix	45-47	3
β-strand	48-50	3	12
β-strand	53	1	13
β-strand	60-64	5	12
β-strand	69-72	4	12
α-helix	73-74	2
β-strand	78-82	5	12
β-strand	85-96	12	12
β-strand	98	1	14
β-strand	101	1	14
β-strand	107-108	2	11
β-strand	111-112	2	11
α-helix	113	1
β-strand	115-123	9	12
α-helix	129-132	4
β-strand	139-149	11	12
α-helix	154-160	7
α-helix	163-166	4
β-strand	172-175	4	12
β-strand	179	1	13
α-helix	180-183	4
β-strand	191-197	7	12
β-strand	205-212	8	12
β-strand	216-219	4	12
α-helix	220-228	9
β-strand	231	1	15
β-strand	237	1	15
α-helix	243-245	3
β-strand	254-255	2	12

Chain D: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	32-33	2	16
α-helix	35-37	3
β-strand	39-40	2	17
β-strand	48-50	3	17
β-strand	53	1	18
β-strand	60-64	5	17
β-strand	69-72	4	17
α-helix	73	1
β-strand	78-82	5	17
β-strand	85-96	12	17
β-strand	98	1	19
β-strand	101	1	19
β-strand	107-108	2	16
β-strand	111-112	2	16
α-helix	113	1
β-strand	115-123	9	17
α-helix	129-132	4
β-strand	139-148	10	17
α-helix	154-160	7
α-helix	164-166	3
β-strand	172-175	4	17
β-strand	179	1	18
α-helix	180-183	4
β-strand	191-196	6	17
β-strand	207-212	6	17
β-strand	216-218	3	17
α-helix	220-228	9
β-strand	231	1	20
β-strand	237	1	20
α-helix	243-245	3
β-strand	254-255	2	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Carbonic anhydrase 9	A, B, C, D	protein	256	Homo sapiens	Q16790 (AlphaFold model)

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

>9R8Y_1 Carbonic anhydrase 9 (chains A, B, C, D)
GDQSHWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELLGFQLPPLPELRL
RNNGHSVQLTLPPGLEMALGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHL
STAFARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISA
LLPSDFSRYFQYEGSLTTPPCAQGVIWTVFQQTVMLSAKQLHTLSDTLWGPGDSRLQLNF
RATQPLNGRVIEASFP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
A1JDL	~{N}-butyl-4-cyclohexylsulfanyl-3-sulfamoyl-benzamide	C17 H26 N2 O3 S2	4

Primary citation

Affinity and Selectivity of Protein-Ligand Recognition: A Minor Chemical Modification Changes Carbonic Anhydrase Binding Profile. Zaksauskas, A., Paketuryte-Latve, V., Jankunaite, A. et al. J Med Chem (2025) 68:17752-17773. DOI 10.1021/acs.jmedchem.5c01421 · PubMed

Other PDB entries of the same protein (UniProt Q16790 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RQQ 1.28 Å, X-ray crystal structure of protiated (H) large monoclinic unit cell CA IX SV.
6RQU 1.39 Å, X-ray crystal structure of H/D exchanged (H/D) small monoclinic unit cell CA IX SV.
6RQW 1.49 Å, X-ray crystal structure of perdeuterated (D) small monoclinic unit cell CA IX SV.
6Y74 1.53 Å, X-ray crystal structure of human carbonic anhydrase IX catalytic domain.
5DVX 1.6 Å, Crystal structure of the catalytic-domain of human carbonic anhydrase IX at 1.6 angstrom…
6G9U 1.75 Å, Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide
6RQN 1.78 Å, X-ray crystal structure of protiated (H) small monoclinic unit cell CA IX SV.
5FL4 1.82 Å, Three dimensional structure of human carbonic anhydrase IX in complex with…
6FE2 1.87 Å, Three dimensional structure of human carbonic anhydrase IX
6FE0 1.91 Å, Three dimensional structure of human carbonic anhydrase IX in complex with…
5FL6 1.95 Å, Three dimensional structure of human carbonic anhydrase IX in complex with…
6FE1 1.95 Å, Three dimensional structure of human carbonic anhydrase IX in complex with…

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