6QN5: Carbonic anhydrase 9

Three dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide. Determined by X-ray diffraction at 1.96 Å resolution. Released 26 Feb 2020.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,590
Mol. weight: 114.56 kDa
Ligands: J8N, ZN
Released: 26 Feb 2020

Explore 6QN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QN5 contains 53 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: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	15	1
α-helix	16-19	4
α-helix	21-24	4
β-strand	32-33	2	1
α-helix	35-37	3
α-helix	38	1
β-strand	39-40	2	2
α-helix	45-47	3
β-strand	48-50	3	2
β-strand	52	1	3
β-strand	57-61	5	2
β-strand	66-69	4	2
α-helix	70-71	2
β-strand	78-82	5	2
β-strand	86-97	12	2
β-strand	99	1	4
β-strand	102	1	4
β-strand	108-109	2	1
β-strand	112-113	2	1
α-helix	114	1
β-strand	116-124	9	2
α-helix	131-134	4
β-strand	141-150	10	2
α-helix	155-161	7
α-helix	164-167	4
β-strand	173-176	4	2
β-strand	180	1	3
α-helix	181-184	4
β-strand	191-197	7	2
β-strand	205-212	8	2
β-strand	216-218	3	2
α-helix	220-227A	9
β-strand	230	1	5
β-strand	236	1	5
α-helix	242-244	3
β-strand	253-254	2	2

Chain B: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
α-helix	21-24	4
β-strand	32-33	2	6
α-helix	35-37	3
β-strand	39-40	2	7
α-helix	45-47	3
β-strand	48-50	3	7
β-strand	52	1	8
β-strand	57-61	5	7
β-strand	66-69	4	7
β-strand	78-82	5	7
β-strand	86-97	12	7
β-strand	99	1	9
β-strand	102	1	9
β-strand	108-109	2	6
β-strand	112-113	2	6
α-helix	114	1
β-strand	116-124	9	7
α-helix	131-134	4
β-strand	141-150	10	7
α-helix	153-154	2
α-helix	155-161	7
α-helix	165-167	3
β-strand	173-176	4	7
β-strand	180	1	8
α-helix	181-184	4
β-strand	191-197	7	7
β-strand	205-212	8	7
β-strand	216-218	3	7
α-helix	220-226	7
β-strand	230-231	2	10
β-strand	235-236	2	10
α-helix	242-244	3
β-strand	253-254	2	7

Chain C: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
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	52	1	13
β-strand	57-61	5	12
β-strand	66-69	4	12
α-helix	70-71	2
β-strand	78-82	5	12
β-strand	86-97	12	12
β-strand	99	1	14
β-strand	102	1	14
β-strand	108-109	2	11
β-strand	112-113	2	11
α-helix	114	1
β-strand	116-124	9	12
α-helix	131-134	4
β-strand	141-151	11	12
α-helix	155-161	7
α-helix	165-167	3
β-strand	173-176	4	12
β-strand	180	1	13
α-helix	181-184	4
β-strand	191-197	7	12
β-strand	205-212	8	12
β-strand	216-219	4	12
α-helix	220-227A	9
β-strand	230	1	15
β-strand	236	1	15
α-helix	242-244	3
α-helix	250-252	3
β-strand	253-254	2	12

Chain D: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
α-helix	21-24	4
β-strand	32-33	2	16
α-helix	35-37	3
β-strand	39-40	2	17
α-helix	45-47	3
β-strand	48-50	3	17
β-strand	52	1	18
β-strand	57-61	5	17
β-strand	66-69	4	17
α-helix	70-71	2
β-strand	78-82	5	17
β-strand	86-97	12	17
β-strand	99	1	19
β-strand	102	1	19
β-strand	108-109	2	16
β-strand	112-113	2	16
α-helix	114	1
β-strand	116-124	9	17
α-helix	131-134	4
β-strand	141-150	10	17
α-helix	155-161	7
α-helix	164-167	4
β-strand	173-176	4	17
β-strand	180	1	18
α-helix	181-184	4
β-strand	191-197	7	17
β-strand	205-212	8	17
β-strand	216-218	3	17
α-helix	220-227A	9
β-strand	230	1	20
β-strand	236	1	20
α-helix	242-244	3
α-helix	250-252	3
β-strand	253-254	2	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Carbonic anhydrase 9	A, B, C, D	protein	257	Homo sapiens	Q16790 (AlphaFold model)

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

>6QN5_1 Carbonic anhydrase 9 (chains A, B, C, D)
GPDQSHWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELLGFQLPPLPELR
LRNNGHSVQLTLPPGLEMALGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVH
LSTAFARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDIS
ALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVMLSAKQLHTLSDTLWGPGDSRLQLN
FRATQPLNGRVIEASFP

Ligands and cofactors

ID	Name	Formula	Copies
J8N	4-chloranyl-~{N}-(3-oxidanylpropyl)-2-phenylsulfanyl-5-sulfamoyl-benzamide	C16 H17 Cl N2 O4 S2	4
ZN	Zinc ion	Zn	4

Primary citation

Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. Zaksauskas, A., Capkauskaite, E., Jezepcikas, L. et al. Eur J Med Chem (2020) 185:111825-111825. DOI 10.1016/j.ejmech.2019.111825 · 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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