SAXSdb — 5jvt

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

Friend leukemia integration 1 transcription factor

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 276–375	Not recorded	;DNA (5'-D(GPAPCPCPGPGPAPAPGPTPG)-3') ; × 1 ;DNA (5'-D(CPAPCPTPTPCPCPGPGPTPC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6	Resolution 3.10 Å R-free 0.237
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain D； UniProt 276–375	Not recorded	;DNA (5'-D(GPAPCPCPGPGPAPAPGPTPG)-3') ; × 1 ;DNA (5'-D(CPAPCPTPTPCPCPGPGPTPC)-3') ; × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6	Resolution 3.10 Å R-free 0.237
3	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain G； UniProt 276–375	Not recorded	;DNA (5'-D(GPAPCPCPGPGPAPAPGPTPG)-3') ; × 1 ;DNA (5'-D(CPAPCPTPTPCPCPGPGPTPC)-3') ; × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6	Resolution 3.10 Å R-free 0.237

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 5JVT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLI DNA-BINDING DOMAIN OF FLI-1 Deposited 1994-09-15	Different construct 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 276–373（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1X66 Solution structure of the SAM_PNT-domain of the human friend LEUKEMIAINTEGRATION 1 transcription factor Deposited 2005-05-17	Different construct 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 114–198（85 aa） Fragment：SAM_PNT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient NMR sample composition 1.17mM SAM_PNT DOMAIN, 20mM TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2YTU Solution structure of the SAM_PNT-domain of the human friend LEUKEMIAINTEGRATION 1 transcription factor Deposited 2007-04-05	Different construct 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 100–220（121 aa） Fragment：SAM_PNT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120 mM；Pressure AMBIENT NMR sample composition 0.24mM SAM_PNT DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5E8G Crystal structure of the DNA binding domain of human transcription factor FLI1 Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–399（124 aa） Fragment：UNP residues 276-399 Chain C 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M sodium acetate pH 5.5, 0.1 M Co2+ sulfate heptahydrate, 24% PEG 4000	Resolution 2.70 Å R-free 0.248
5E8G Crystal structure of the DNA binding domain of human transcription factor FLI1 Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 276–399（124 aa） Fragment：UNP residues 276-399 Chain D 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M sodium acetate pH 5.5, 0.1 M Co2+ sulfate heptahydrate, 24% PEG 4000	Resolution 2.70 Å R-free 0.248
5E8I Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA ACCGGAAGTG Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 276–399（124 aa） Fragment：UNP residues 276-399 Chain G 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Na cacodylate pH 6.5, 0.2 M CaCl2, 14% w/v PEG 8000	Resolution 3.45 Å R-free 0.271
5E8I Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA ACCGGAAGTG Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain D 276–399（124 aa） Fragment：UNP residues 276-399 Chain J 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Na cacodylate pH 6.5, 0.2 M CaCl2, 14% w/v PEG 8000	Resolution 3.45 Å R-free 0.271
6VG2 Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 276–375（100 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；1.6 M ammonium sulfate	Resolution 3.90 Å R-free 0.294
6VG2 Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 276–375（100 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；1.6 M ammonium sulfate	Resolution 3.90 Å R-free 0.294
6VG8 Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 276–375（100 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；7% w/v PEG 4000, 50 mM Na Citrate, pH 5.6, 4% v/v isopropanol	Resolution 4.31 Å R-free 0.283
6VGD Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 276–375（100 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.20 Å R-free 0.293
9CP6 Crystal structure of the DNA binding domain of FLI1 (residues 259-371) Deposited 2024-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 259–371（113 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Hepes, pH 6.5, 1 M Na citrate	Resolution 1.66 Å R-free 0.235
9MWY Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing four contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain C 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain D 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain L 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399)	Mutation：F362A Mutation：F362A Mutation：F362A Mutation：F362A	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Tris, pH 6.5, 0.7 M sodium acetate	Resolution 3.28 Å R-free 0.281
9MX8 Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing three contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 259–375（117 aa） Fragment：DNA-binding domain (residues 259-375) Chain C 259–375（117 aa） Fragment：DNA-binding domain (residues 259-375) Chain D 259–375（117 aa） Fragment：DNA-binding domain (residues 259-375)	Mutation：F362A Mutation：F362A Mutation：F362A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M sodium cacodylate, pH 7.0, 1.6 M sodium acetate, added cryoprotectant: 34% sucrose	Resolution 3.15 Å R-free 0.278
9MX9 Crystal structure of the DNA binding domain of FLI1 (F362A) in complex with a DNA containing two contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain D 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399)	Mutation：F362A Mutation：F362A	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 18% PEG8000	Resolution 2.55 Å R-free 0.250
9MXA Crystal structure of the DNA binding domain of FLI1 (wild-type) in complex with a DNA containing two contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain D 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1 M Tris, pH 8.5, 2 M ammonium phosphate	Resolution 2.59 Å R-free 0.287

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

View Construct and Data Evidence

UniProt name	FLI1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–104； UniProt 276–375 Author chain D； PDBConstruct 5–104； UniProt 276–375 Author chain G； PDBConstruct 5–104； UniProt 276–375

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	5jvt
Deposition date deposition_date	2016-05-11
Structure title title	Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG
Keywords keywords	transcription, DNA binding, cancer, Ewing sarcoma, transcription-dna complex; transcription/dna
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	30.37 Å
Radius of gyration Rg (electron density) rg_electron	29.08 Å
Forward intensity I(0) i0	71051800.00
Molecular weight molecular_weight	53246.0 kDa
Excluded volume excluded_volume	60821 Å³
Envelope volume envelope_volume	82577 Å³
Hydration-shell volume shell_volume	24801 Å³
Envelope diameter envelope_diameter	98.6 Å
Shell Rg shell_rg	34.57 Å
Envelope Rg envelope_rg	28.76 Å
Shape Rg shape_rg	28.98 Å
Total Rg total_rg	29.74 Å
Total atoms total_atoms	3675
Residues n_residues	348
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	94.8 Å
Rg (real space) rg_real	30.48 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	7.1050e+07
I(0) uncertainty (real space) i0_real_error	1.1290e+06
Rg (reciprocal space) rg_reciprocal	30.43 Å
I(0) (reciprocal space) i0_reciprocal	71050000.0000
Solution quality estimate total_estimate	0.8392
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.693
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5748000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.297

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Friend leukemia integration 1 transcription factor
Molecular weight formula_weight	12098.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	3677

GPHMPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPTE

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 polymer

Description description	;DNA (5'-D(GPAPCPCPGPGPAPAPGPTP*G)-3') ;
Molecular weight formula_weight	3423.2 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E,H

GACCGGAAGTG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPAPCPTPTPCPCPGPGPTP*C)-3') ;
Molecular weight formula_weight	3285.1 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F,I

CACTTCCGGTC

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5jvtA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5jvtD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5jvtG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	191.845 Å
Unit-cell length b length_b	191.845 Å
Unit-cell length c length_c	87.556 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	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1963
R_work r_work	0.1941
R_free r_free	0.2372

fit	/app/data/saxs_computation/jv/5jvt/5jvt.fit
pddf	/app/data/pr_computation/jv/5jvt/5jvt.pr.out
profile	/app/data/saxs_computation/jv/5jvt/5jvt.dat

Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG

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

Friend leukemia integration 1 transcription factor

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 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)