5DVX: Catalytic-domain of human carbonic anhydrase IX

Crystal structure of the catalytic-domain of human carbonic anhydrase IX at 1.6 angstrom resolution. Determined by X-ray diffraction at 1.6 Å resolution. Released 3 Aug 2016.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,847
Mol. weight: 58.08 kDa
Ligands: ZN
Released: 3 Aug 2016

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

Secondary structure: helices and β-sheets

5DVX contains 26 α-helices and 44 β-strands across 2 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	149-152	4
α-helix	154-157	4
β-strand	165-166	2	1
α-helix	168-170	3
α-helix	171	1
β-strand	172-173	2	2
α-helix	178-180	3
β-strand	181-183	3	2
β-strand	186	1	3
β-strand	193-197	5	2
β-strand	202-205	4	2
α-helix	206-207	2
β-strand	211-215	5	2
β-strand	218-229	12	2
β-strand	231	1	4
β-strand	234	1	4
β-strand	240-241	2	1
β-strand	244-245	2	1
α-helix	246	1
β-strand	248-256	9	2
α-helix	262-265	4
β-strand	272-281	10	2
α-helix	287-293	7
α-helix	297-299	3
β-strand	305-308	4	2
β-strand	312	1	3
α-helix	313-316	4
β-strand	324-330	7	2
β-strand	338-345	8	2
β-strand	349-351	3	2
α-helix	353-361	9
β-strand	364	1	5
β-strand	370	1	5
α-helix	376-378	3
α-helix	384-386	3
β-strand	387-388	2	2

Chain B: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	149-151	3
α-helix	154-157	4
β-strand	165-166	2	6
α-helix	168-170	3
β-strand	172-173	2	7
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	186	1	8
β-strand	193-197	5	7
β-strand	202-205	4	7
α-helix	206-207	2
β-strand	211-215	5	7
β-strand	218-229	12	7
β-strand	231	1	9
β-strand	234	1	9
β-strand	240-241	2	6
β-strand	244-245	2	6
β-strand	248-256	9	7
α-helix	262-265	4
β-strand	272-281	10	7
α-helix	287-293	7
α-helix	297-299	3
β-strand	305-308	4	7
β-strand	312	1	8
α-helix	313-316	4
β-strand	324-330	7	7
β-strand	338-345	8	7
β-strand	349-351	3	7
α-helix	353-361	9
β-strand	364	1	10
β-strand	370	1	10
α-helix	376-378	3
α-helix	384-386	3
β-strand	387-388	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Carbonic anhydrase 9	A, B	protein	260	Homo sapiens	Q16790 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DVX_1 Carbonic anhydrase 9 (chains A, B)
HWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELSGFQLPPLPELRLRNNG
HSVQLTLPPGLEMKLGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHLSTKY
ARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISALLPS
DFSRYFQYEGSLTTPPCAQGVIWTVFNQTVSLSAKQLHTLSDTLWGPGDSRLQLNFRATQ
PLNGRVIEASFPAGVDSSPR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (TRS, CL, GOL) are not listed.

Primary citation

The Structure of Carbonic Anhydrase IX Is Adapted for Low-pH Catalysis. Mahon, B.P., Bhatt, A., Socorro, L. et al. Biochemistry (2016) 55:4642-4653. DOI 10.1021/acs.biochem.6b00243 · 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.
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…
6QN2 1.95 Å, Three dimensional structure of human carbonic anhydrase IX in complex with…

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