SAXSdb — 6z2j

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone deacetylase 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 1–482 Chain E； UniProt 1–482	Not recorded	Deoxynucleotidyltransferase terminal-interacting protein 1 × 2 （Q9H147） Mitotic deacetylase-associated SANT domain protein × 2 （Q6PJG2） IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Blot time 3 sec, blot force 10.	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6Z2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BKX The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex Deposited 2013-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–482（482 aa）	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 2 K POTASSIUM ION × 4 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400	Resolution 3.00 Å R-free 0.261
5ICN HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4 Deposited 2016-02-23	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–376（376 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400	Resolution 3.30 Å R-free 0.299
6Z2K The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex Deposited 2020-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 1–482（482 aa） Chain E 1–482（482 aa） Chain I 1–482（482 aa） Chain K 1–482（482 aa）	Not recorded	ZN ZINC ION × 4 K POTASSIUM ION × 8 IHP INOSITOL HEXAKISPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot time 3 sec, blot force 10.	Resolution 4.50 Å
7AO8 Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex Deposited 2020-10-14	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–482（482 aa） Chain E 1–482（482 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10	Resolution 4.50 Å
7AO9 Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex Deposited 2020-10-14	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–482（482 aa） Chain E 1–482（482 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10	Resolution 6.10 Å
7AOA Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex Deposited 2020-10-14	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–482（482 aa） Chain E 1–482（482 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds, blot force 10	Resolution 19.40 Å
7SME p107 pocket domain complexed with HDAC1 peptide Deposited 2021-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 413–422（10 aa） Fragment：UNP residues 413-422	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.64 Å R-free 0.277
8VOJ The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6 Deposited 2024-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–482（482 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
8VPQ The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML Deposited 2024-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–482（482 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8VRT The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant Deposited 2024-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–482（482 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
9R4I An auto inhibitory loop in the MiDAC histone deacetylase complex Deposited 2025-05-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–482（482 aa） Chain D 1–482（482 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES, 25 mM KCl, 1 micromolar Inositol Hexaphosphate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HDAC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–482； UniProt 1–482 Author chain E； PDBConstruct 1–482； UniProt 1–482

Deoxynucleotidyltransferase terminal-interacting protein 1

Homo sapiens

UniProt Q9H147

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–130 Chain B； UniProt 1–130	Not recorded	Histone deacetylase 1 × 2 （Q13547） Mitotic deacetylase-associated SANT domain protein × 2 （Q6PJG2） IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Blot time 3 sec, blot force 10.	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6Z2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MWI The structure of the carboxy-terminal domain of DNTTIP1 Deposited 2014-11-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 197–316（120 aa） Fragment：carboxy-terminal domain (UNP residues 197-316)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 80；Pressure ambient NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 80；Pressure ambient NMR sample composition 0.3 mM [U-100% 13C; U-100% 15N] DNTTIP1(197-316), 40 mM potassium phosphate, 1 mM DTT, 1 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-100% 13C; U-100% 15N] DNTTIP1(197-316), 40 mM potassium phosphate, 1 mM DTT, 1 mM sodium azide, 100% D2O \| 100% D2O	Resolution not provided
4D6K Structure of DNTTIP1 dimerisation domain. Deposited 2014-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 56–147（92 aa） Fragment：DIMERISATION DOMAIN Chain B 56–147（92 aa） Fragment：DIMERISATION DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；295 K；100 MM SODIUM ACETATE PH 4.6 14% PROPAN-2-OL	Resolution 2.10 Å R-free 0.224
4D6K Structure of DNTTIP1 dimerisation domain. Deposited 2014-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 56–147（92 aa） Fragment：DIMERISATION DOMAIN Chain F 56–147（92 aa） Fragment：DIMERISATION DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；295 K；100 MM SODIUM ACETATE PH 4.6 14% PROPAN-2-OL	Resolution 2.10 Å R-free 0.224
4D6K Structure of DNTTIP1 dimerisation domain. Deposited 2014-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 56–147（92 aa） Fragment：DIMERISATION DOMAIN Chain D 56–147（92 aa） Fragment：DIMERISATION DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；295 K；100 MM SODIUM ACETATE PH 4.6 14% PROPAN-2-OL	Resolution 2.10 Å R-free 0.224
6Z2K The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex Deposited 2020-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–130（130 aa） Chain B 1–130（130 aa） Chain G 1–130（130 aa） Chain H 1–130（130 aa）	Not recorded	ZN ZINC ION × 4 K POTASSIUM ION × 8 IHP INOSITOL HEXAKISPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot time 3 sec, blot force 10.	Resolution 4.50 Å
9R4I An auto inhibitory loop in the MiDAC histone deacetylase complex Deposited 2025-05-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–329（329 aa） Chain F 1–329（329 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES, 25 mM KCl, 1 micromolar Inositol Hexaphosphate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TDIF1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 1–130 Author chain B； PDBConstruct 1–130； UniProt 1–130

Mitotic deacetylase-associated SANT domain protein

Homo sapiens

UniProt Q6PJG2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 717–887 Chain F； UniProt 717–887	Not recorded	Histone deacetylase 1 × 2 （Q13547） Deoxynucleotidyltransferase terminal-interacting protein 1 × 2 （Q9H147） IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Blot time 3 sec, blot force 10.	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6Z2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6Z2K The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex Deposited 2020-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 717–887（171 aa） Chain F 717–887（171 aa） Chain J 717–887（171 aa） Chain L 717–887（171 aa）	Not recorded	ZN ZINC ION × 4 K POTASSIUM ION × 8 IHP INOSITOL HEXAKISPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot time 3 sec, blot force 10.	Resolution 4.50 Å
9R4I An auto inhibitory loop in the MiDAC histone deacetylase complex Deposited 2025-05-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 628–887（260 aa） Chain E 628–887（260 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 K POTASSIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES, 25 mM KCl, 1 micromolar Inositol Hexaphosphate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MDEAS_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 3–173； UniProt 717–887 Author chain F； PDBConstruct 3–173； UniProt 717–887

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6z2j
Deposition date deposition_date	2020-05-16
Structure title title	The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex
Keywords keywords	HDAC1 MIDEAS ELMSAN1 DNTTIP1 TDIF1 histone deacetylase MiDAC, GENE REGULATION; GENE REGULATION
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	53.70 Å
Radius of gyration Rg (electron density) rg_electron	54.39 Å
Forward intensity I(0) i0	273994000.00
Molecular weight molecular_weight	136620.0 kDa
Excluded volume excluded_volume	170430 Å³
Envelope volume envelope_volume	255570 Å³
Hydration-shell volume shell_volume	42780 Å³
Envelope diameter envelope_diameter	172.9 Å
Shell Rg shell_rg	49.43 Å
Envelope Rg envelope_rg	53.31 Å
Shape Rg shape_rg	54.38 Å
Total Rg total_rg	54.26 Å
Total atoms total_atoms	18847
Residues n_residues	1185
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	159.6 Å
Rg (real space) rg_real	54.33 Å
Rg uncertainty (real space) rg_real_error	1.89 Å
I(0) (real space) i0_real	2.7400e+08
I(0) uncertainty (real space) i0_real_error	5.7360e+06
Rg (reciprocal space) rg_reciprocal	53.12 Å
I(0) (reciprocal space) i0_reciprocal	273500000.0000
Solution quality estimate total_estimate	0.6193
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	-1.069
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24740000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.265; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.252; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Histone deacetylase 1
Molecular weight formula_weight	55178.9 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E
Atom count atom_count	18888

MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKLA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Deoxynucleotidyltransferase terminal-interacting protein 1
Molecular weight formula_weight	14381.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MGATGDAEQPRGPSGAERGGLELGDAGAAGQLVLTNPWNIMIKHRQVQRRGRRSQMTTSFTDPAISMDLLRAVLQPSINEEIQTVFNKYMKFFQKAALNVRDNVGEEVDAEQLIQEACRSCLEQAKLLFS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Mitotic deacetylase-associated SANT domain protein
Molecular weight formula_weight	19794.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,D

GAVSIEPRINVGSRFQAEIPLMRDRALAAADPHKADLVWQPWEDLESSREKQRQVEDLLTAACSSIFPGAGTNQELALHCLHESRGDILETLNKLLLKKPLRPHNHPLATYHYTGSDQWKMAERKLFNKGIAIYKKDFFLVQKLIQTKTVAQCVEFYYTYKKQVKIGRNGTLT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6z2jC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z2jE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	126484

fit	/app/data/saxs_computation/z2/6z2j/6z2j.fit
pddf	/app/data/pr_computation/z2/6z2j/6z2j.pr.out
profile	/app/data/saxs_computation/z2/6z2j/6z2j.dat

The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone deacetylase 1

State in the Current Structure

Other States of the Same Protein in the Database

Deoxynucleotidyltransferase terminal-interacting protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Mitotic deacetylase-associated SANT domain protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)