SAXSdb — 2znr

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

AMSH-like protease

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 264–436	Fragment：MPN domain, DUB domain, Unp residues 264-436	ZN ZINC ION × 2 PR PRASEODYMIUM ION × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；45mM sodium acetate buffer (pH 4.6), 22% PEG 4000, 90mM ammonium acetate, 10mM praseodymium (III) acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.20 Å R-free 0.165

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 2ZNR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZNV Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer Deposited 2008-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 264–436（173 aa） Fragment：MPN domain, DUB domain, UNP residues 264-436	Mutation：E292A	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
2ZNV Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer Deposited 2008-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 264–436（173 aa） Fragment：MPN domain, DUB domain, UNP residues 264-436	Mutation：E292A	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
7L97 Crystal structure of STAMBPL1 in complex with an engineered binder Deposited 2021-01-02	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 263–436（174 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20% PEG 1500, 0.2M NaCl, 0.1M HEPES pH7.5	Resolution 2.01 Å R-free 0.214

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STALP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–178； UniProt 264–436

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	2znr
Deposition date deposition_date	2008-05-01
Structure title title	Crystal structure of the DUB domain of human AMSH-LP
Keywords keywords	metal binding protein, Alternative splicing, Hydrolase, Metal-binding, Metalloprotease, Protease, Ubl conjugation pathway, Zinc; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	17.39 Å
Radius of gyration Rg (electron density) rg_electron	16.14 Å
Forward intensity I(0) i0	8179710.00
Molecular weight molecular_weight	20647.0 kDa
Excluded volume excluded_volume	25720 Å³
Envelope volume envelope_volume	30054 Å³
Hydration-shell volume shell_volume	15544 Å³
Envelope diameter envelope_diameter	60.6 Å
Shell Rg shell_rg	22.39 Å
Envelope Rg envelope_rg	16.66 Å
Shape Rg shape_rg	16.11 Å
Total Rg total_rg	17.31 Å
Total atoms total_atoms	1427
Residues n_residues	178
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	59.1 Å
Rg (real space) rg_real	17.29 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	8.1800e+06
I(0) uncertainty (real space) i0_real_error	9.3220e+04
Rg (reciprocal space) rg_reciprocal	17.30 Å
I(0) (reciprocal space) i0_reciprocal	8180000.0000
Solution quality estimate total_estimate	0.7903
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.170
Kurtosis Kurtosis kurtosis	-0.283
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1300000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	AMSH-like protease
Molecular weight formula_weight	19974.3 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1732

GPGHMEGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSACKKKGFHPHTKEPRLFSICKHVLVKDIKIIVLDLR

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	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	PRASEODYMIUM ION
Molecular weight formula_weight	140.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2znra1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d2znra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2znrA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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8. Citations (1)

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Unit-cell length a length_a	81.865 Å
Unit-cell length b length_b	81.865 Å
Unit-cell length c length_c	64.693 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	31.090 Å
R factor r_factor	0.1496
R_work r_work	0.1488
R_free r_free	0.1655

fit	/app/data/saxs_computation/zn/2znr/2znr.fit
pddf	/app/data/pr_computation/zn/2znr/2znr.pr.out
profile	/app/data/saxs_computation/zn/2znr/2znr.dat

Crystal structure of the DUB domain of human AMSH-LP

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

AMSH-like protease

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