3kci

The third RLD domain of HERC2

Method: X-RAY DIFFRACTION D_max: 58.0 Å Quality: EXCELLENT

▼

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

Probable E3 ubiquitin-protein ligase HERC2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 3951–4321	Fragment：UNP RESIDUES 3951-4321, RCC1-LIKE DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；290.9 K；20% PEG3350, 0.2mM MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.9K	Resolution 1.80 Å R-free 0.195

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 3KCI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KEO Solution NMR structure of human protein HS00059, cytochrome-b5-like domain of the HERC2 E3 ligase. Northeast structural genomics consortium (NESG) target ht98a Deposited 2009-01-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1203–1296（94 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N] hs00059-1, 10 mM TRIS-2, 300 mM sodium chloride-3, 10 uM ZnSO4-4, 10 mM DTT-5, 0.01 % NaN3-6, 10 mM benzamidine-7, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 417–790（374 aa）	Not recorded	SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.60 Å R-free 0.238
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 417–790（374 aa）	Not recorded	SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.60 Å R-free 0.238
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 417–790（374 aa）	Not recorded	SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.60 Å R-free 0.238
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2702–2755（54 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000	Resolution 2.10 Å R-free 0.227
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2702–2755（54 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000	Resolution 2.10 Å R-free 0.227
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2702–2751（50 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000	Resolution 2.25 Å R-free 0.243
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2702–2751（50 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000	Resolution 2.25 Å R-free 0.243
7Q40 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 Deposited 2021-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.35 Å R-free 0.230
7Q40 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 Deposited 2021-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.35 Å R-free 0.230
7Q40 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 Deposited 2021-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.35 Å R-free 0.230
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 3.01 Å R-free 0.255
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 3.01 Å R-free 0.255
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 3.01 Å R-free 0.255
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 1.95 Å R-free 0.206
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 1.95 Å R-free 0.206
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 1.95 Å R-free 0.206
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.40 Å R-free 0.265
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.40 Å R-free 0.265
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.40 Å R-free 0.265
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate	Resolution 2.20 Å R-free 0.231
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate	Resolution 2.20 Å R-free 0.231
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate	Resolution 2.20 Å R-free 0.231
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.10 Å R-free 0.224
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.10 Å R-free 0.224
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.10 Å R-free 0.224
7Q46 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
7Q46 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein Deposited 2021-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
7Q46 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
7RGW Crystal structure of HERC2 DOC domain Deposited 2021-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2759–2914（156 aa） Fragment：DOC domain (UNP residues 2759-2914)	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M HEPES, pH 7.5, 25% PEG3350	Resolution 1.99 Å R-free 0.213
9L8Y Crystal structure of HERC2 Deposited 2024-12-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2539–2700（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；289 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3,350	Resolution 1.92 Å R-free 0.206
9L93 Crystal structure of NCOA4 in complex with HERC2 Deposited 2024-12-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2539–2700（162 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000	Resolution 1.73 Å R-free 0.207
9L93 Crystal structure of NCOA4 in complex with HERC2 Deposited 2024-12-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2539–2700（162 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000	Resolution 1.73 Å R-free 0.207

14 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HERC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–389； UniProt 3951–4321

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3kci
Deposition date deposition_date	2009-10-21
Structure title title	The third RLD domain of HERC2
Keywords keywords	;WD40, RCC1, STRUCTURAL GENOMICS CONSORTIUM, SGC, Coiled coil, Ligase, Metal-binding, Phosphoprotein, Ubl conjugation pathway, WD repeat, Zinc, Zinc-finger ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.00 Å
Radius of gyration Rg (electron density) rg_electron	18.96 Å
Forward intensity I(0) i0	26797200.00
Molecular weight molecular_weight	38227.0 kDa
Excluded volume excluded_volume	47158 Å³
Envelope volume envelope_volume	53148 Å³
Hydration-shell volume shell_volume	22455 Å³
Envelope diameter envelope_diameter	58.1 Å
Shell Rg shell_rg	26.18 Å
Envelope Rg envelope_rg	19.12 Å
Shape Rg shape_rg	18.96 Å
Total Rg total_rg	19.82 Å
Total atoms total_atoms	2686
Residues n_residues	366
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

▼

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

Maximum dimension Dmax dmax	58.0 Å
Rg (real space) rg_real	19.85 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.6800e+07
I(0) uncertainty (real space) i0_real_error	2.9520e+05
Rg (reciprocal space) rg_reciprocal	19.88 Å
I(0) (reciprocal space) i0_reciprocal	26800000.0000
Solution quality estimate total_estimate	0.9131
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.7 Å
Skewness Skewness skewness	0.038
Kurtosis Kurtosis kurtosis	-0.595
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7411000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.989

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3kciA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

▶

8. Citations (1)

▶

Unit-cell length a length_a	52.673 Å
Unit-cell length b length_b	52.673 Å
Unit-cell length c length_c	215.242 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1538
R_work r_work	0.1516
R_free r_free	0.1950

Description description	Probable E3 ubiquitin-protein ligase HERC2
Molecular weight formula_weight	41116.0 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3139

The third RLD domain of HERC2

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

Probable E3 ubiquitin-protein ligase HERC2

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	366

fit	/app/data/saxs_computation/kc/3kci/3kci.fit
pddf	/app/data/pr_computation/kc/3kci/3kci.pr.out
profile	/app/data/saxs_computation/kc/3kci/3kci.dat