SAXSdb — 1cmx

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

PROTEIN (UBIQUITIN YUH1-UBAL)

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–235 Chain C； UniProt 1–235	Fragment：ALL	PROTEIN (UBIQUITIN YUH1-UBAL) × 2 （P02248）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5	Resolution 2.25 Å R-free 0.285

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 1CMX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7EN4 Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase. Deposited 2021-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–236（236 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM [U-100% 15N] ubiquitin hydrolase, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBL1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 1–235 Author chain C； PDBConstruct 1–235； UniProt 1–235

PROTEIN (UBIQUITIN YUH1-UBAL)

OrganismNot specified

UniProt P02248

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–75 Chain D； UniProt 1–75	Fragment：ALL Non-standard monomer：Yes (specific site not provided by mmCIF)	PROTEIN (UBIQUITIN YUH1-UBAL) × 2 （P35127）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5	Resolution 2.25 Å R-free 0.285

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 1CMX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GJZ Solution structure of a dimeric N-terminal fragment of human ubiquitin Deposited 2001-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：RESIDUES 1-51 Chain B 1–51（51 aa） Fragment：RESIDUES 1-51	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 800MM SODIUM SULPHATE；Pressure 1	Resolution not provided
1UD7 SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7 Deposited 1999-04-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–116（76 aa）	Mutation：I3V,V5L,I13V,L15I,I23V,V26F,I67L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；303 K；Pressure 1	Resolution not provided
1UZX A complex of the Vps23 UEV with ubiquitin Deposited 2004-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22% PEG 8000, 0.1M MES PH 6.5, 0.2M (NH4)2SO4	Resolution 1.85 Å R-free 0.274

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

View Construct and Data Evidence

UniProt name	UBIQ_HUMANX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–75 Author chain D； PDBConstruct 1–76； UniProt 1–75

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	1cmx
Deposition date deposition_date	1999-05-12
Structure title title	STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES
Keywords keywords	UBIQUITIN HYDROLASE, UBIQUITIN, DEUBIQUITINATING ENZYME, CYSTEINE PROTEASE, ENZYME SPECIFICITY, HYDROLASE; 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	26.87 Å
Radius of gyration Rg (electron density) rg_electron	25.78 Å
Forward intensity I(0) i0	53234400.00
Molecular weight molecular_weight	57591.0 kDa
Excluded volume excluded_volume	72448 Å³
Envelope volume envelope_volume	87488 Å³
Hydration-shell volume shell_volume	28798 Å³
Envelope diameter envelope_diameter	87.5 Å
Shell Rg shell_rg	32.65 Å
Envelope Rg envelope_rg	25.98 Å
Shape Rg shape_rg	25.77 Å
Total Rg total_rg	26.55 Å
Total atoms total_atoms	4067
Residues n_residues	515
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	88.0 Å
Rg (real space) rg_real	26.90 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	5.3230e+07
I(0) uncertainty (real space) i0_real_error	7.0660e+05
Rg (reciprocal space) rg_reciprocal	26.89 Å
I(0) (reciprocal space) i0_reciprocal	53230000.0000
Solution quality estimate total_estimate	0.7012
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	86.5 Å
Skewness Skewness skewness	0.370
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	18930000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 0.199; Positv: 1.000; Valcen: 0.951; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (UBIQUITIN YUH1-UBAL)
Molecular weight formula_weight	26276.1 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4142

MSGENRAVVPIESNPEVFTNFAHKLGLKNEWAYFDIYSLTEPELLAFLPRPVKAIVLLFPINEDRKSSTSQQITSSYDVIWFKQSVKNACGLYAILHSLSNNQSLLEPGSDLDNFLKSQSDTSSSKNRFDDVTTDQFVLNVIKENVQTFSTGQSEAPEATADTNLHYITYVEENGGIFELDGRNLSGPLYLGKSDPTATDLIEQELVRVRVASYMENANEEDVLNFAMLGLGPNW

Entity 2 Entity 2 polymer

Description description	PROTEIN (UBIQUITIN YUH1-UBAL)
Molecular weight formula_weight	8560.8 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	75

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1cmxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.6 — Ubiquitin carboxyl-terminal hydrolase UCH-L

Domain ID domain_id	d1cmxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d1cmxc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.6 — Ubiquitin carboxyl-terminal hydrolase UCH-L

Domain ID domain_id	d1cmxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (3 domains)

Domain ID domain_id	1cmxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

Domain ID domain_id	1cmxB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	1cmxC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

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8. Citations (2)

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Unit-cell length a length_a	199.300 Å
Unit-cell length b length_b	199.300 Å
Unit-cell length c length_c	36.800 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2480
R_free r_free	0.2850

fit	/app/data/saxs_computation/cm/1cmx/1cmx.fit
pddf	/app/data/pr_computation/cm/1cmx/1cmx.pr.out
profile	/app/data/saxs_computation/cm/1cmx/1cmx.dat

STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES

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

PROTEIN (UBIQUITIN YUH1-UBAL)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (UBIQUITIN YUH1-UBAL)

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)