5FL4: Carbonic anhydrase 9

Three dimensional structure of human carbonic anhydrase IX in complex with 5-(1-naphthalen-1-yl-1,2,3-triazol-4-yl)thiophene-2-sulfonamide. Determined by X-ray diffraction at 1.82 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 8,966
Mol. weight: 115.11 kDa
Ligands: ZN, 9FK
Released: 11 Nov 2015

Explore 5FL4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FL4 contains 53 α-helices and 86 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: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16	1
α-helix	17-20	4
α-helix	22-25	4
β-strand	33-34	2	1
β-strand	40-41	2	2
α-helix	46-48	3
β-strand	49-51	3	2
β-strand	54	1	3
β-strand	61-65	5	2
β-strand	70-73	4	2
α-helix	74-75	2
β-strand	79-81	3	2
β-strand	87-97	11	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	130-133	4
β-strand	140-149	10	2
α-helix	155-161	7
α-helix	165-167	3
β-strand	173-176	4	2
β-strand	180	1	3
α-helix	181-184	4
β-strand	192-198	7	2
β-strand	206-213	8	2
α-helix	216	1
β-strand	217-219	3	2
α-helix	221-229	9
β-strand	232	1	5
β-strand	238	1	5
α-helix	244-246	3
β-strand	255-256	2	2

Chain B: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
α-helix	22-25	4
β-strand	33-34	2	6
α-helix	36-38	3
β-strand	40-41	2	7
α-helix	46-48	3
β-strand	49-51	3	7
β-strand	54	1	8
β-strand	61-65	5	7
β-strand	70-73	4	7
α-helix	74-75	2
β-strand	79-83	5	7
β-strand	86-97	12	7
β-strand	108-109	2	6
β-strand	112-113	2	6
α-helix	114	1
β-strand	116-124	9	7
α-helix	130-133	4
β-strand	140-149	10	7
α-helix	153-154	2
α-helix	155-161	7
α-helix	164-167	4
β-strand	173-176	4	7
β-strand	180	1	8
α-helix	181-184	4
β-strand	192-198	7	7
β-strand	206-213	8	7
β-strand	217-219	3	7
α-helix	221-229	9
β-strand	232	1	9
β-strand	238	1	9
α-helix	244-246	3
β-strand	255-256	2	7

Chain C: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16	1
α-helix	17-20	4
α-helix	22-25	4
β-strand	33-34	2	10
α-helix	36-38	3
β-strand	40-41	2	11
α-helix	46-48	3
β-strand	49-51	3	11
β-strand	54	1	12
β-strand	61-65	5	11
β-strand	70-73	4	11
α-helix	74-75	2
β-strand	79-83	5	11
β-strand	86-97	12	11
β-strand	99	1	13
β-strand	102	1	13
β-strand	108-109	2	10
β-strand	112-113	2	10
α-helix	114	1
β-strand	116-124	9	11
α-helix	130-133	4
β-strand	140-150	11	11
α-helix	155-161	7
α-helix	165-167	3
β-strand	173-176	4	11
β-strand	180	1	12
α-helix	181-184	4
β-strand	192-198	7	11
β-strand	206-213	8	11
β-strand	217-220	4	11
α-helix	221-230	10
β-strand	232-233	2	14
β-strand	237-238	2	14
α-helix	244-246	3
β-strand	255-256	2	11

Chain D: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	16	1
α-helix	17-20	4
α-helix	22-25	4
β-strand	33-34	2	15
β-strand	40-41	2	16
α-helix	46-48	3
β-strand	49-51	3	16
β-strand	54	1	17
β-strand	61-65	5	16
β-strand	70-73	4	16
α-helix	74-75	2
β-strand	79-83	5	16
β-strand	86-97	12	16
β-strand	99	1	18
β-strand	102	1	18
β-strand	108-109	2	15
β-strand	112-113	2	15
α-helix	114	1
β-strand	116-124	9	16
α-helix	130-133	4
β-strand	140-149	10	16
α-helix	153-154	2
α-helix	155-161	7
α-helix	164-167	4
β-strand	173-176	4	16
β-strand	180	1	17
α-helix	181-184	4
β-strand	192-198	7	16
β-strand	206-213	8	16
β-strand	217-219	3	16
α-helix	221-229	9
β-strand	232	1	19
β-strand	238	1	19
α-helix	244-246	3
α-helix	252-254	3
β-strand	255-256	2	16

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

>5FL4_1 CARBONIC ANHYDRASE 9 (chains A, B, C, D)
GPDQSHWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELLGFQLPPLPELR
LRNNGHSVQLTLPPGLEMALGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVH
LSTAFARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDIS
ALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVMLSAKQLHTLSDTLWGPGDSRLQLN
FRATQPLNGRVIEASFP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
9FK	5-(1-naphthalen-1-yl-1,2,3-triazol-4-yl)thiophene-2-sulfonamide	C16 H12 N4 O2 S2	4

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

Primary citation

An Efficient Expression and Crystallization System of the Cancer Asociated Carbonic Anhydrase Isoform Ix. Leitans, J., Kazaks, A., Balode, A. et al. J Med Chem (2015) 58:9004. DOI 10.1021/ACS.JMEDCHEM.5B01343 · 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.
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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