SAXSdb — 6rml

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

DNA topoisomerase 2-binding protein 1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–290 Chain B； UniProt 1–290	Not recorded	53BP1 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；287.15 K；10% w/v PEG 20 000 20% v/v PEG MME 550 0.03 M of each ethylene glycol 0.1 M MES/imidazole pH 6.5	Resolution 2.81 Å R-free 0.260

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 6RML	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WF6 The third BRCA1 C-terminus (BRCT) domain of Similar to S.pombe rad4+/cut5+ product Deposited 2004-05-26	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 354–472（119 aa） Fragment：BRCA1 C-turminus (BRCT) domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 220mM；Pressure ambient NMR sample composition 1.06mM 13C/15N-labeled protein; 20mM d-TRIS, 200mM NaCl, 1mM d-DTT, and 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2XNH Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1 Deposited 2010-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–287（287 aa） Fragment：BRCT 0,1 AND 2, RESIDUES 1-287	Non-standard monomer：Yes (specific site not provided by mmCIF)	IOD IODIDE ION × 17	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；0.1M TRIS-HCL PH 6.8, 0.5M KI, 5% (V/V) GLYCEROL, 22.5% (W/V), 10% PEG 3350	Resolution 2.80 Å R-free 0.251
2XNK Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1 Deposited 2010-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–290（290 aa） Fragment：BRCT 0,1 AND 2, RESIDUES 1-290	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS-HCL PH 7.5, 0.4 M MGCL2, 25% PEG 4000, 4% GLYCEROL, 0.01 M SPERMIDINE TETRA-HCL	Resolution 2.60 Å R-free 0.266
2XNK Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1 Deposited 2010-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–290（290 aa） Fragment：BRCT 0,1 AND 2, RESIDUES 1-290	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS-HCL PH 7.5, 0.4 M MGCL2, 25% PEG 4000, 4% GLYCEROL, 0.01 M SPERMIDINE TETRA-HCL	Resolution 2.60 Å R-free 0.266
2XNK Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1 Deposited 2010-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–290（290 aa） Fragment：BRCT 0,1 AND 2, RESIDUES 1-290	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS-HCL PH 7.5, 0.4 M MGCL2, 25% PEG 4000, 4% GLYCEROL, 0.01 M SPERMIDINE TETRA-HCL	Resolution 2.60 Å R-free 0.266
2XNK Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1 Deposited 2010-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–290（290 aa） Fragment：BRCT 0,1 AND 2, RESIDUES 1-290	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS-HCL PH 7.5, 0.4 M MGCL2, 25% PEG 4000, 4% GLYCEROL, 0.01 M SPERMIDINE TETRA-HCL	Resolution 2.60 Å R-free 0.266
3AL2 Crystal Structure of TopBP1 BRCT7/8 Deposited 2010-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1264–1493（230 aa） Fragment：BRCT7 and BRCT8, UNP residues 1264-1493	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Li2SO4, Tris-HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.204
3AL3 Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex Deposited 2010-07-22	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 A 1264–1493（230 aa） Fragment：BRCT7 and BRCT8, UNP residues 1264-1493	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Sodium formate, pH 8, vapor diffusion, hanging drop, temperature 298K	Resolution 2.15 Å R-free 0.236
3JVE Crystal Structure of the Sixth BRCT Domain of TopBP1 Deposited 2009-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 893–996（104 aa） Fragment：C-terminus (BRCT) domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；0.1M Tris-HCl pH 6.8, PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.34 Å R-free 0.173
3OLC Crystal structure of the N-terminal region of TopBP1 Deposited 2010-08-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–290（290 aa） Fragment：N-terminal domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1M MES, 11%(w/v) PEG3350, 0.85M sodium nitrate, 2mM EDTA, 4mM DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.40 Å R-free 0.258
3PD7 Crystal Structure of the Sixth BRCT Domain of Human TopBP1 Deposited 2010-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 893–994（102 aa） Fragment：Sixth BRCT domain, UNP residues 893-994	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；20% PEG 4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.26 Å R-free 0.144
3PD7 Crystal Structure of the Sixth BRCT Domain of Human TopBP1 Deposited 2010-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 893–994（102 aa） Fragment：Sixth BRCT domain, UNP residues 893-994	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；20% PEG 4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.26 Å R-free 0.144
3UEN Crystal structure of TopBP1 BRCT4/5 domains Deposited 2011-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 549–746（198 aa） Fragment：BRCT domain	Not recorded	SCN THIOCYANATE ION × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 3350, NaSCN, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.224
3UEO Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide Deposited 2011-10-31	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 549–746（198 aa） Fragment：BRCT domain Chain C 549–746（198 aa） Fragment：BRCT domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 10000, Ammonium acetate, bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.234
3UEO Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide Deposited 2011-10-31	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 549–746（198 aa） Fragment：BRCT domain Chain D 549–746（198 aa） Fragment：BRCT domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 10000, Ammonium acetate, bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.234
6RMM Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide Deposited 2019-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 548–741（194 aa） Chain B 548–741（194 aa） Chain C 548–741（194 aa） Chain D 548–741（194 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287.15 K；10% w/v PEG 4000, 20% v/v glycerol 0.02 M of each carboxylic acid 0.1 M MOPS/HEPES-Na pH 7.5	Resolution 3.53 Å R-free 0.234
7CMZ Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8 Deposited 2020-07-29	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 A 1264–1493（230 aa）	Not recorded	K POTASSIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic	Resolution 1.70 Å R-free 0.215
9MAT TopBP1 BRCT 7-8 Domain Deposited 2025-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1264–1493（230 aa）	Not recorded	MLA MALONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.3 M Sodium malonate pH 7.0, 20% w/v PEG 3350	Resolution 1.65 Å R-free 0.207
9MAW Crystal structure of TOPBP1BRCT7-8 domain in complex with 1-Adamantaneacetic acid Deposited 2025-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1264–1491（228 aa）	Not recorded	A1ENP 1-Adamantylacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Citric acid, 2.4 M Ammonium sulfate pH 5.0	Resolution 2.45 Å R-free 0.237

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

View Construct and Data Evidence

UniProt name	TOPB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–292； UniProt 1–290 Author chain B； PDBConstruct 3–292； UniProt 1–290

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	6rml
Deposition date deposition_date	2019-05-07
Structure title title	Crystal structure of TOPBP1 BRCT0,1,2 in complex with a 53BP1 phosphopeptide
Keywords keywords	BRCT domain Phosphopeptide recognition, SIGNALING PROTEIN; SIGNALING PROTEIN
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	31.78 Å
Radius of gyration Rg (electron density) rg_electron	31.15 Å
Forward intensity I(0) i0	67185500.00
Molecular weight molecular_weight	65629.0 kDa
Excluded volume excluded_volume	82591 Å³
Envelope volume envelope_volume	111180 Å³
Hydration-shell volume shell_volume	30907 Å³
Envelope diameter envelope_diameter	103.2 Å
Shell Rg shell_rg	36.71 Å
Envelope Rg envelope_rg	30.96 Å
Shape Rg shape_rg	31.13 Å
Total Rg total_rg	31.76 Å
Total atoms total_atoms	4593
Residues n_residues	564
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	100.1 Å
Rg (real space) rg_real	31.71 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	6.7190e+07
I(0) uncertainty (real space) i0_real_error	9.5410e+05
Rg (reciprocal space) rg_reciprocal	31.74 Å
I(0) (reciprocal space) i0_reciprocal	67190000.0000
Solution quality estimate total_estimate	0.9051
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.0 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.715
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10710000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.930

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 2-binding protein 1
Molecular weight formula_weight	33891.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	4605

GPMSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPEA

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	53BP1
Molecular weight formula_weight	1755.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EVEEIPETPCESQGE

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6rmlA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	6rmlA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	6rmlB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	6rmlB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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8. Citations (1)

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Unit-cell length a length_a	84.440 Å
Unit-cell length b length_b	84.440 Å
Unit-cell length c length_c	225.190 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	69.550 Å
R factor r_factor	0.2247
R_work r_work	0.2229
R_free r_free	0.2597

fit	/app/data/saxs_computation/rm/6rml/6rml.fit
pddf	/app/data/pr_computation/rm/6rml/6rml.pr.out
profile	/app/data/saxs_computation/rm/6rml/6rml.dat

Crystal structure of TOPBP1 BRCT0,1,2 in complex with a 53BP1 phosphopeptide

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

DNA topoisomerase 2-binding protein 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)