SAXSdb — 1ify

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

UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A

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 156–204	Fragment：INTERNAL UBA DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；300 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 100mM sodium chloride；Pressure ambient NMR sample composition：2mM UBA1 U-15N,13C \| 50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O NMR sample composition：2mM UBA1 U-15N \| 50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O NMR sample composition：2mM UBA1 \| 50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O	Resolution not provided

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 1IFY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DV0 Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A) Deposited 2000-01-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 319–363（45 aa） Fragment：UBA DOMAIN (C-TERMINAL DOMAIN)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 100mM sodium chloride；Pressure ambient NMR sample composition 1mM Uba-domain, chemically synthesized; 50mM potassium phosphate pH 6.5; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM Uba-domain, expressed in E.coli, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 2mM Uba-domain, U-15N, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 2mM Uba-domain, U-15N,13C, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1F4I SOLUTION STRUCTURE OF THE HHR23A UBA(2) MUTANT P333E, DEFICIENT IN BINDING THE HIV-1 ACCESSORY PROTEIN VPR Deposited 2000-06-07	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 319–363（45 aa） Fragment：C-TERMINAL UBA DOMAIN	Mutation：P333E	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 150mM sodium chloride；Pressure ambient NMR sample composition 2mM UBA(2) domain mutant P333E; 50mM phosphate buffer, 150mM sodium chloride; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1OQY Structure of the DNA repair protein hHR23a Deposited 2003-03-11	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition 0.5 mM 13C,15N,2H hHR23a; 20 mM NaPO4 pH 6.5; 100 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1P98 High-resolution NMR structure of the Ubl-domain of HHR23A Deposited 2003-05-09	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–78（78 aa） Fragment：Ubiquitin-like domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure ambient NMR sample composition 2mM ubiquitin-like domain of HHR23A U-15N,13C \| 50mM sodium phosphate, 100mM sodium chloride, pH 6.5, 5% D2O NMR sample composition 2mM ubiquitin-like domain of HHR23A, unlabeled \| 50mM sodium phosphate, 100mM sodium chloride, pH 6.5, 5% D2O	Resolution not provided
1P9D High-resolution structure of the complex of HHR23A ubiquitin-like domain and the C-terminal ubiquitin-interacting motif of proteasome subunit S5a Deposited 2003-05-10	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 1–78（78 aa） Fragment：ubiquitin-like domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure ambient NMR sample composition 2mM S5a peptide unlabeled, 2mM ubiquitin-like domain of HHR23A U-15N,13C \| 50mM sodium phosphate, 100mM sodium chloride, 5% D2O NMR sample composition 2mM S5a peptide U-15N,13C, 2mM ubiquitin-like domain of HHR23A unlabeled \| 50mM sodium phosphate, 100mM sodium chloride, 5% D2O	Resolution not provided
1QZE HHR23a protein structure based on residual dipolar coupling data Deposited 2003-09-16	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–363（362 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition 0.55 MM 15N, HHR23A; 20MM NAPO4 PH 6.5; 100 MM NACL;7.5 mg/ml Pf1 phage; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1TP4 Solution structure of the XPC binding domain of hHR23A protein Deposited 2004-06-15	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 223–317（95 aa） Fragment：XPC binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 20mM sodium phosphate, 122mM sodium chloride, 0.05% sodium azide；Pressure ambient NMR sample composition 1mM XPCB U-15N,13C, 20mM sodium phosphate, 122mM sodium chloride, 0.05% sodium azide \| 95% H2O/5% D2O	Resolution not provided
2WYQ THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23) Deposited 2009-11-19	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 1–82（82 aa） Fragment：UBIQUITIN-LIKE DOMAIN, RESIDUES 1-82	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE	Resolution 1.65 Å R-free 0.160
2WYQ THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23) Deposited 2009-11-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–82（82 aa） Fragment：UBIQUITIN-LIKE DOMAIN, RESIDUES 1-82	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE	Resolution 1.65 Å R-free 0.160
5XBO Lanthanoid tagging via an unnatural amino acid for protein structure characterization Deposited 2017-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–204（49 aa） Fragment：UNP residues 156-204	Not recorded	TB TERBIUM(III) ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 760 NMR sample composition 20mM HEPES, 100mM sodium chloride, 10% D2O, 0.2mM [U-99% 15N] ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20mM HEPES, 100mM sodium chloride, 0.1mM [U-99% 15N] HHR23A UBA1 Domain, 0.1 mM ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6W2G Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell Deposited 2020-03-05	Different construct Different mutation/modification 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 155–204（50 aa）	Mutation：Y188G	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol	Resolution 1.10 Å R-free 0.153
6W2G Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell Deposited 2020-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 155–204（50 aa）	Mutation：Y188G	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol	Resolution 1.10 Å R-free 0.153
6W2H Crystal Structure of the Internal UBA Domain of HHR23A Deposited 2020-03-05	Different construct 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 155–204（50 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH 8.5, 1.5 M Ammonium sulfate, 12%(v/v) Glycerol	Resolution 1.60 Å R-free 0.205
6W2I Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A Deposited 2020-03-05	Different construct Different mutation/modification 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 155–204（50 aa）	Mutation：Y188G	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0M Ammonium sulfate X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0M Ammonium sulfate	Resolution 1.45 Å R-free 0.183
6XQI Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09	Different construct 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 F 319–358（40 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M Tris, pH 7.5, 10% PEG 4000	Resolution 2.34 Å R-free 0.220
6XQI Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 319–358（40 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M Tris, pH 7.5, 10% PEG 4000	Resolution 2.34 Å R-free 0.220
6XQJ Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 223–363（141 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 927 uM [U-100% 2H; U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1100 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1110 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1000 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 745 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
7TGP E176T/Y188G variant of the internal UBA Domain of HHR23A Deposited 2022-01-08	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 155–204（50 aa） Fragment：residues 154-204 of the Internal UBA domain	Mutation：E176T, Y188G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；sodium formate	Resolution 1.40 Å R-free 0.175
8Q06 EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A Deposited 2023-07-27	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 C 1–84（84 aa） Chain D 1–84（84 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M potassium chloride, 2.2 M ammonium sulphate	Resolution 1.90 Å R-free 0.247

16 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RD23A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–49； UniProt 156–204

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	1ify
Deposition date deposition_date	2001-04-13
Structure title title	Solution Structure of the Internal UBA Domain of HHR23A
Keywords keywords	Ubiquitin associated domain, UBA domain, Ubiquitin proteosome pathway, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	10.29 Å
Radius of gyration Rg (electron density) rg_electron	10.15 Å
Forward intensity I(0) i0	45793600.00
Molecular weight molecular_weight	54892.0 kDa
Excluded volume excluded_volume	68295 Å³
Envelope volume envelope_volume	12205 Å³
Hydration-shell volume shell_volume	8836 Å³
Envelope diameter envelope_diameter	40.8 Å
Shell Rg shell_rg	17.41 Å
Envelope Rg envelope_rg	13.16 Å
Shape Rg shape_rg	10.12 Å
Total Rg total_rg	10.61 Å
Total atoms total_atoms	7649
Residues n_residues	490
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	39.8 Å
Rg (real space) rg_real	10.30 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	4.5790e+07
I(0) uncertainty (real space) i0_real_error	5.4560e+05
Rg (reciprocal space) rg_reciprocal	10.30 Å
I(0) (reciprocal space) i0_reciprocal	45790000.0000
Solution quality estimate total_estimate	0.7661
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	12.6 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	0.176
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	72270.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.362; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ifya_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

CATH v4.4 (1 domains)

Domain ID domain_id	1ifyA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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8. Citations (2)

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Description description	UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
Molecular weight formula_weight	5496.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7649

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

fit	/app/data/saxs_computation/if/1ify/1ify.fit
pddf	/app/data/pr_computation/if/1ify/1ify.pr.out
profile	/app/data/saxs_computation/if/1ify/1ify.dat

Solution Structure of the Internal UBA Domain of HHR23A

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

UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)