SAXSdb — 4i1s

▼

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

Melanoma differentiation associated protein-5

Sus scrofa

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 303–397 Chain A； UniProt 666–808	Fragment：helicase domain region 641-665 replaced by SGSGS, proteolysis by trypsin during crystallization Non-standard monomer：Yes (specific site not provided by mmCIF)	Non-structural protein V × 1 （P11207） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH7.5 18% (w/v) PEG1500 trace amounts of trypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.29 Å R-free 0.230

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A7LCX1_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 303–397 Author chain A； PDBConstruct 101–243； UniProt 666–808

Non-structural protein V

Simian virus 5

UniProt P11207

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–52	Fragment：region 55-79 replaced by SGSGSGSGSG, proteolysis by trypsin during crystallization	Melanoma differentiation associated protein-5 × 1 （A7LCX1） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH7.5 18% (w/v) PEG1500 trace amounts of trypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.29 Å R-free 0.230

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 4I1S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2B5L Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein Deposited 2005-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–222（222 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20000, sodium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.299
2B5L Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein Deposited 2005-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–222（222 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20000, sodium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.299
2HYE Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex Deposited 2006-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–222（222 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.316

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

View Construct and Data Evidence

UniProt name	V_SV5
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–52； UniProt 1–52

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4i1s
Deposition date deposition_date	2012-11-21
Structure title title	Melanoma differentiation associated protein-5 Helicase domain complex with inhibitor Non-structural protein V
Keywords keywords	SF2-ATPase, Helicase, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.22 Å
Radius of gyration Rg (electron density) rg_electron	21.13 Å
Forward intensity I(0) i0	21571500.00
Molecular weight molecular_weight	34040.0 kDa
Excluded volume excluded_volume	42016 Å³
Envelope volume envelope_volume	50316 Å³
Hydration-shell volume shell_volume	20526 Å³
Envelope diameter envelope_diameter	72.7 Å
Shell Rg shell_rg	26.93 Å
Envelope Rg envelope_rg	21.24 Å
Shape Rg shape_rg	21.04 Å
Total Rg total_rg	22.14 Å
Total atoms total_atoms	2361
Residues n_residues	284
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	72.2 Å
Rg (real space) rg_real	22.25 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.1570e+07
I(0) uncertainty (real space) i0_real_error	2.8240e+05
Rg (reciprocal space) rg_reciprocal	22.25 Å
I(0) (reciprocal space) i0_reciprocal	21570000.0000
Solution quality estimate total_estimate	0.8924
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.376
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3545000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.971

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Melanoma differentiation associated protein-5
Molecular weight formula_weight	28586.8 kDa
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	2489

EDLFKDRLLEIMTNIQTFCQISPMSDFGTQPYEQWLIQMEKKAARDGNRKDRVCAEHLKKYNEALQINDTIRRIDAYNHLKTFYNDEKEKKFEVLSGSGSLDESDIFLMTLFLRNKKILKKLAENPEYENEKLTKLRNTIMEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPMTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVT

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	pigs,swine,wild boar
NCBI Class编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Non-structural protein V
Molecular weight formula_weight	5844.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GGFHRREYSIGWVGDEVKVTEWCNPSCSPITAAARRFECTCHQCPVTCSECE

来源 Source

来源生物 organism	Simian virus 5
通用名 common_name	SV5
NCBI Class编号 ncbi_taxonomy_id	11208
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

▼

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4i1sA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1320 — phosphoenolpyruvate carboxylase, domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4i1sA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4i1sB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	340 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	51.070 Å
Unit-cell length b length_b	52.490 Å
Unit-cell length c length_c	120.790 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.293 Å
Low-resolution limit resolution_low	48.141 Å
R factor r_factor	0.1817
R_work r_work	0.1792
R_free r_free	0.2296

fit	/app/data/saxs_computation/i1/4i1s/4i1s.fit
pddf	/app/data/pr_computation/i1/4i1s/4i1s.pr.out
profile	/app/data/saxs_computation/i1/4i1s/4i1s.dat

Melanoma differentiation associated protein-5 Helicase domain complex with inhibitor Non-structural protein V

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

Melanoma differentiation associated protein-5

State in the Current Structure

Other States of the Same Protein in the Database

Non-structural protein V

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)