SAXSdb — 2qk0

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

CAP-Gly domain-containing linker 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 57–128	Fragment：Cap-Gly domain 1 Mutation：L124M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；1.2 M Sodium malonate, 100 mM Glycine, 1.1 mM Lanthanum chloride, Protein concentration 15 mg/ml, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233

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 2QK0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CP5 Solution structure of the 1st CAP-Gly domain in human CLIP-170/restin Deposited 2005-05-19	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 1–128（128 aa） Fragment：CAP-Gly domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1mM protein, 20mM d-Tris-HCl, pH7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CP6 Solution structure of the 2nd CAP-Gly domain in human CLIP-170/restin Deposited 2005-05-19	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 181–339（159 aa） Fragment：CAP-Gly domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1mM protein, 20mM d-Tris-HCl, pH7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2E3H Crystal structure of the CLIP-170 CAP-Gly domain 2 Deposited 2006-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 211–300（90 aa） Fragment：CAP-Gly domain 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.45 Å R-free 0.215
2E3I Crystal structure of the CLIP-170 CAP-Gly domain 1 Deposited 2006-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 56–141（86 aa） Fragment：CAP-Gly domain 1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.00 Å R-free 0.259
2E4H Solution structure of cytoskeletal protein in complex with tubulin tail Deposited 2006-12-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 203–300（98 aa） Fragment：CAP-Gly domain 2, residues 203-300	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；303 K；Pressure ambient NMR sample composition 0.9mM U-15N,13C CLIP: Nonlabel tubulin; 30mM BisTris buffer K; 1mM DTT; 100% D2O \| 100% D2O NMR sample composition 0.9mM U-15N CLIP: Nonlabel tubulin; 30mM BisTris buffer K; 1mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9mM U-15N,13C tubulin: Nonlabel CLIP; 30mM BisTris buffer K; 1mM DTT; 100% D2O \| 100% D2O NMR sample composition 0.9mM U-15N tubulin: Nonlabel CLIP; 30mM BisTris buffer K; 1mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2HQH Crystal structure of p150Glued and CLIP-170 Deposited 2006-07-18	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 E 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.215
2HQH Crystal structure of p150Glued and CLIP-170 Deposited 2006-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.215
2HQH Crystal structure of p150Glued and CLIP-170 Deposited 2006-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.215
2HQH Crystal structure of p150Glued and CLIP-170 Deposited 2006-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.215
2HQH Crystal structure of p150Glued and CLIP-170 Deposited 2006-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain E 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427 Chain F 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427 Chain G 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427 Chain H 1405–1427（23 aa） Fragment：second zinc finger domain, residues 1405-1427	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.215
3E2U Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED) Deposited 2008-08-06	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 E 1388–1427（40 aa） Fragment：Zn-knuckle 2	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.2M Trisodium Citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.238
3E2U Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED) Deposited 2008-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1388–1427（40 aa） Fragment：Zn-knuckle 2	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.2M Trisodium Citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.238
3E2U Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED) Deposited 2008-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1388–1427（40 aa） Fragment：Zn-knuckle 2	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.2M Trisodium Citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.238
3E2U Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED) Deposited 2008-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1388–1427（40 aa） Fragment：Zn-knuckle 2	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.2M Trisodium Citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.238
3E2U Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED) Deposited 2008-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1388–1427（40 aa） Fragment：Zn-knuckle 2 Chain F 1388–1427（40 aa） Fragment：Zn-knuckle 2 Chain G 1388–1427（40 aa） Fragment：Zn-knuckle 2 Chain H 1388–1427（40 aa） Fragment：Zn-knuckle 2	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.2M Trisodium Citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.238
3RDV Structure of the SLAIN2c-CLIPCG1 complex Deposited 2011-04-01	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 56–127（72 aa） Fragment：CAP-Gly 1 domain, residues 56-127	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；36% PEG 6000, 100mM citric acid, pH 4.5, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.229
3RDV Structure of the SLAIN2c-CLIPCG1 complex Deposited 2011-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 56–127（72 aa） Fragment：CAP-Gly 1 domain, residues 56-127	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；36% PEG 6000, 100mM citric acid, pH 4.5, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.229
3RDV Structure of the SLAIN2c-CLIPCG1 complex Deposited 2011-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 56–127（72 aa） Fragment：CAP-Gly 1 domain, residues 56-127	Not recorded	BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；36% PEG 6000, 100mM citric acid, pH 4.5, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.229
3RDV Structure of the SLAIN2c-CLIPCG1 complex Deposited 2011-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 56–127（72 aa） Fragment：CAP-Gly 1 domain, residues 56-127	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；36% PEG 6000, 100mM citric acid, pH 4.5, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.229

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

View Construct and Data Evidence

UniProt name	CLIP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–74； UniProt 57–128

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	2qk0
Deposition date deposition_date	2007-07-09
Structure title title	Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1
Keywords keywords	CLIP-170, Cap-Gly domain, microtubule plus end, +TIP, PROTEIN BINDING; PROTEIN BINDING
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	12.83 Å
Radius of gyration Rg (electron density) rg_electron	11.44 Å
Forward intensity I(0) i0	1466750.00
Molecular weight molecular_weight	8121.0 kDa
Excluded volume excluded_volume	10156 Å³
Envelope volume envelope_volume	11062 Å³
Hydration-shell volume shell_volume	8484 Å³
Envelope diameter envelope_diameter	37.9 Å
Shell Rg shell_rg	16.74 Å
Envelope Rg envelope_rg	11.80 Å
Shape Rg shape_rg	11.43 Å
Total Rg total_rg	12.83 Å
Total atoms total_atoms	571
Residues n_residues	72
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	40.1 Å
Rg (real space) rg_real	12.76 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	1.4670e+06
I(0) uncertainty (real space) i0_real_error	1.5320e+04
Rg (reciprocal space) rg_reciprocal	12.77 Å
I(0) (reciprocal space) i0_reciprocal	1467000.0000
Solution quality estimate total_estimate	0.9046
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.7 Å
Skewness Skewness skewness	0.155
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	224400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qk0a1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.10 — Cap-Gly domain
Family Family family	b.34.10.1 — Cap-Gly domain

Domain ID domain_id	d2qk0a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2qk0A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	190 — CAP Gly-rich-like domain

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8. Citations (1)

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Unit-cell length a length_a	27.242 Å
Unit-cell length b length_b	42.533 Å
Unit-cell length c length_c	51.806 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	2.000 Å
Low-resolution limit resolution_low	32.880 Å
R factor r_factor	—
R_work r_work	0.1730
R_free r_free	0.2330

Description description	CAP-Gly domain-containing linker protein 1
Molecular weight formula_weight	8243.2 kDa
Mutation mutation	L124M
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	637

Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1

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

CAP-Gly domain-containing linker 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

fit	/app/data/saxs_computation/qk/2qk0/2qk0.fit
pddf	/app/data/pr_computation/qk/2qk0/2qk0.pr.out
profile	/app/data/saxs_computation/qk/2qk0/2qk0.dat