3ZNR: HDAC7

HDAC7 bound with inhibitor TMP269. Determined by X-ray diffraction at 2.4 Å resolution. Released 27 Mar 2013.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 8,454
Mol. weight: 137.7 kDa
Ligands: NU9, ZN
Released: 27 Mar 2013

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

Secondary structure: helices and β-sheets

3ZNR contains 67 α-helices and 55 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: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	520-523	4	1
α-helix	526-530	5
α-helix	546-557	12
β-strand	565-567	3	1
α-helix	571-573	3
α-helix	574-578	5
α-helix	583-590	8
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	684-694	11
β-strand	701-705	5	1
α-helix	712-717	6
β-strand	724-731	8	1
α-helix	733-735	3
α-helix	750-752	3
β-strand	756-761	6	1
α-helix	768-769	2
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
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	862-865	4
α-helix	866-868	3
α-helix	875-877	3
α-helix	878-891	14
α-helix	896-898	3

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	519	1
β-strand	520-523	4	8
α-helix	526-530	5
α-helix	546-557	12
α-helix	561-563	3
β-strand	564-567	4	8
α-helix	571-573	3
α-helix	574-577	4
α-helix	583-590	8
α-helix	601-607	7
β-strand	615	1	9
β-strand	621-622	2	9
β-strand	628-629	2	9
α-helix	634-653	20
β-strand	659-662	4	8
β-strand	672	1	10
β-strand	675	1	10
β-strand	677	1	11
β-strand	680	1	11
α-helix	684-695	12
β-strand	701-705	5	8
α-helix	712-717	6
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	12
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	13
β-strand	814	1	12
β-strand	815	1	13
α-helix	817-827	11
α-helix	830-833	4
β-strand	835-839	5	8
α-helix	845-860	16
α-helix	866-868	3
α-helix	871-873	3
α-helix	875-877	3
α-helix	878-891	14
α-helix	896-898	3

Chain C: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	520-523	4	14
α-helix	526-530	5
α-helix	546-557	12
β-strand	565-567	3	14
α-helix	571-573	3
α-helix	574-578	5
α-helix	583-590	8
β-strand	622	1	15
β-strand	628	1	15
α-helix	634-653	20
β-strand	659-662	4	14
β-strand	672	1	16
β-strand	675	1	16
α-helix	684-694	11
β-strand	701-705	5	14
α-helix	712-717	6
β-strand	724-731	8	14
α-helix	750-752	3
β-strand	756-761	6	14
α-helix	768-769	2
β-strand	770	1	17
α-helix	771-777	7
α-helix	778-782	5
α-helix	783-789	7
β-strand	793-798	6	14
β-strand	803	1	18
β-strand	814	1	17
β-strand	815	1	18
α-helix	817-828	12
α-helix	831-833	3
β-strand	835-839	5	14
α-helix	845-859	15
α-helix	862-864	3
α-helix	866-868	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 7	A, B, C	protein	423	HOMO SAPIENS	Q8WUI4 (AlphaFold model)

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

>3ZNR_1 HISTONE DEACETYLASE 7 (chains A, B, C)
GSRAQSSPAAPASLSAPEPASQARVLSSSETPARTLPFTTGLIYDSVMLKHQCSCGDNSR
HPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLD
NGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNG
FAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQ
DPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRI
VVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVLALE
GGHDLTAICDASEACVAALLGNRVDPLSEEGWKQKPNLNAIRSLEAVIRVHSKYWGCMQR
LAS

Ligands and cofactors

ID	Name	Formula	Copies
NU9	N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro-2H-pyran-4-yl]methyl}-3-[5-(trifluo…	C25 H21 F3 N4 O3 S	1
ZN	Zinc ion	Zn	6

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

Primary citation

Selective Class Iia Histone Deacetylase Inhibition Via a Non-Chelating Zinc Binding Group. Lobera, M., Madauss, K.P., Pohlhaus, D.T. et al. Nat Chem Biol (2013) 9:319. DOI 10.1038/NCHEMBIO.1223 · 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
3C0Z 2.1 Å, Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with…
8Q9Q 2.11 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7…
3ZNS 2.45 Å, HDAC7 bound with TFMO inhibitor tmp942

Browse structure collections

About this viewer

MolViewer shows 3ZNR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.