3C0Z: Histone deacetylase 7a

Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with SAHA. Determined by X-ray diffraction at 2.1 Å resolution. Released 19 Feb 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,769
Mol. weight: 137.98 kDa
Ligands: ZN, SHH
Released: 19 Feb 2008

Explore 3C0Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C0Z contains 66 α-helices and 58 β-strands across 3 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: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	520-523	4	1
α-helix	526-530	5
α-helix	538-540	3
α-helix	546-557	12
α-helix	561-563	3
β-strand	565-567	3	1
α-helix	571-573	3
α-helix	574-577	4
α-helix	583-590	8
α-helix	601-609	9
β-strand	615	1	2
β-strand	621	1	2
β-strand	622	1	3
β-strand	628	1	3
α-helix	634-653	20
β-strand	659-662	4	1
β-strand	672	1	4
β-strand	675	1	4
β-strand	677	1	5
β-strand	680	1	5
α-helix	684-695	12
β-strand	701-705	5	1
α-helix	712-718	7
β-strand	724-731	8	1
α-helix	750-752	3
β-strand	756-761	6	1
β-strand	770	1	6
α-helix	771-777	7
α-helix	778-782	5
α-helix	783-789	7
β-strand	793-798	6	1
β-strand	803	1	7
α-helix	808-810	3
β-strand	814	1	6
β-strand	815	1	7
α-helix	817-827	11
α-helix	831-833	3
β-strand	835-839	5	1
α-helix	845-860	16
α-helix	866-868	3
α-helix	870-872	3
α-helix	875-877	3
α-helix	878-891	14
α-helix	896-898	3

Chain B: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	520-523	4	8
α-helix	526-530	5
α-helix	546-557	12
α-helix	561-563	3
β-strand	565-567	3	8
α-helix	571-573	3
α-helix	574-578	5
α-helix	583-590	8
β-strand	615	1	9
β-strand	621	1	9
β-strand	622	1	10
β-strand	628	1	10
α-helix	634-653	20
β-strand	659-662	4	8
β-strand	672	1	11
β-strand	675	1	11
β-strand	677	1	12
β-strand	680	1	12
α-helix	684-694	11
β-strand	701-705	5	8
α-helix	712-718	7
β-strand	724-731	8	8
α-helix	750-752	3
β-strand	756-761	6	8
α-helix	768-769	2
β-strand	770	1	13
α-helix	771-777	7
α-helix	778-782	5
α-helix	783-789	7
β-strand	793-798	6	8
β-strand	803	1	14
β-strand	814	1	13
β-strand	815	1	14
α-helix	817-827	11
α-helix	831-833	3
β-strand	835-839	5	8
α-helix	845-859	15
α-helix	875-877	3
α-helix	878-891	14
α-helix	896-898	3

Chain C: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	520-523	4	15
α-helix	526-530	5
α-helix	546-557	12
α-helix	561-563	3
β-strand	565-567	3	15
α-helix	571-573	3
α-helix	574-578	5
α-helix	583-590	8
β-strand	622	1	16
β-strand	628	1	16
α-helix	634-653	20
β-strand	659-662	4	15
β-strand	672	1	17
β-strand	675	1	17
β-strand	677	1	18
β-strand	680	1	18
α-helix	684-694	11
β-strand	701-705	5	15
α-helix	712-718	7
β-strand	724-731	8	15
α-helix	733-735	3
α-helix	750-752	3
β-strand	756-761	6	15
β-strand	770	1	19
α-helix	771-777	7
α-helix	778-782	5
α-helix	783-789	7
β-strand	793-798	6	15
β-strand	803	1	20
β-strand	814	1	19
β-strand	815	1	20
α-helix	817-828	12
α-helix	831-833	3
β-strand	835-839	5	15
α-helix	845-859	15
α-helix	866-868	3
α-helix	870-872	3
α-helix	875-877	3
α-helix	878-891	14
α-helix	896-898	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 7a	A, B, C	protein	423	Homo sapiens	Q8WUI4 (AlphaFold model)

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

>3C0Z_1 Histone deacetylase 7a (chains A, B, C)
GSRAQSSPAAPASLSAPEPASQARVLSSSETPARTLPFTTGLIYDSVMLKHQCSCGDNSR
HPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLD
NGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNG
FAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQ
DPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRI
VVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVLALE
GGHDLTAICDASEACVAALLGNRVDPLSEEGWKQKPNLNAIRSLEAVIRVHSKYWGCMQR
LAS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
SHH	Octanedioic acid hydroxyamide phenylamide	C14 H20 N2 O3	3

Water and common crystallization additives (K) are not listed.

Primary citation

Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. Schuetz, A., Min, J., Allali-Hassani, A. et al. J Biol Chem (2008) 283:11355-11363. DOI 10.1074/jbc.M707362200 · PubMed

Other PDB entries of the same protein (UniProt Q8WUI4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3C10 2.0 Å, Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with…
3C0Y 2.1 Å, Crystal structure of catalytic domain of human histone deacetylase HDAC7
8Q9Q 2.11 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7…
3ZNR 2.4 Å, HDAC7 bound with inhibitor TMP269
3ZNS 2.45 Å, HDAC7 bound with TFMO inhibitor tmp942

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