SAXSdb — 5ip4

▼

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

Neuronal migration protein doublecortin

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 251–341	Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 251-341	XA4551 NANOBODY AGAINST C-DCX × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；20% PEGMME, 100 mM Bis-Tris pH 6.5	Resolution 1.81 Å R-free 0.246
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 251–341	Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 251-341	XA4551 NANOBODY AGAINST C-DCX × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；20% PEGMME, 100 mM Bis-Tris pH 6.5	Resolution 1.81 Å R-free 0.246

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 5IP4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MJD Structure of N-terminal domain of human doublecortin Deposited 2002-08-27	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 87–192（106 aa） Fragment：N-terminal domain, Residues (45-150)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure ambient NMR sample composition 1mM doublecortin 45-150 U-15N, 13C; 50mM phosphate buffer; 5mMM DTT \| 90% H2O, 10% H2O	Resolution not provided
2BQQ X-ray Structure of the N-terminal Domain of Human Doublecortin Deposited 2005-04-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 45–150（106 aa） Fragment：N-TERMINAL DOMAIN RESIDUES 45-150	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；1.4 M NAH2PO4, 0.35 M K2HPO4, 0.6% PEG 150, SITTING DROP, pH 4.40	Resolution 2.20 Å R-free 0.237
2XRP Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF and 3HKE) Docked into the 8-Angstrom Cryo-EM Map of Doublecortin- Stabilised Microtubules Deposited 2010-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 46–140（95 aa） Fragment：RESIDUES 46-140	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer 80MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP；pH 6.8；80MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.20 Å
4ATU Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) docked into an 8A cryo-EM map of doublecortin-stabilised microtubules reconstructed in absence of kinesin Deposited 2012-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 2–360（359 aa） Fragment：RESIDUES 2-360	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer 20MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP；pH 6.8；20MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP cryo-EM vitrification conditions Cryogen ETHANE；CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT	Resolution 8.30 Å
5IKC X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB Deposited 2016-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 52–140（89 aa） Fragment：N-terminal domain, UNP Residues 133-221	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；unknown	Resolution 2.06 Å R-free 0.265
5IKC X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB Deposited 2016-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 52–140（89 aa） Fragment：N-terminal domain, UNP Residues 133-221	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；unknown	Resolution 2.06 Å R-free 0.265
5IN7 X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-07	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 127–231（105 aa） Fragment：N-TERMINAL DOMAIN, UNP RESIDUES 127-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.48 Å R-free 0.236
5IN7 X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-07	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 127–231（105 aa） Fragment：N-TERMINAL DOMAIN, UNP RESIDUES 127-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.48 Å R-free 0.236
5IO9 X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	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 133–230（98 aa） Fragment：N-TERMINAL DOMAIN, UNP RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 1.30 Å R-free 0.210
5IO9 X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	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 133–230（98 aa） Fragment：N-TERMINAL DOMAIN, UNP RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 1.30 Å R-free 0.210
5IOI X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	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 133–231（99 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.40 Å R-free 0.234
5IOI X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	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 133–231（99 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.40 Å R-free 0.234
5IOI X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 133–231（99 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.40 Å R-free 0.234
5IOI X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 133–231（99 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.40 Å R-free 0.234
5IOI X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 133–231（99 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.40 Å R-free 0.234
5IOI X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 133–231（99 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 133-231	Mutation：K215D, K216D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT	Resolution 2.40 Å R-free 0.234
6FNZ Crystal Structure of domain-swapped C-terminal domain of human doublecortin Deposited 2018-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 174–254（81 aa） Fragment：C-terminal ubiquitin-like domain, UNP residues 174-254 Chain C 174–254（81 aa） Fragment：C-terminal ubiquitin-like domain, UNP residues 174-254	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；20 mg/mL protein and 3x cmc CHAPS in 20mM CAPS/NaOH pH10.5, 100mM NaCl, 5mM TCEP mixed 60-70% with 40-30% reservoir consisting of 0.1M HEPES/NaOH pH7.0, 10% PEG 5000 MME, 5% Tacsimate	Resolution 2.23 Å R-free 0.231
6FNZ Crystal Structure of domain-swapped C-terminal domain of human doublecortin Deposited 2018-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 174–254（81 aa） Fragment：C-terminal ubiquitin-like domain, UNP residues 174-254 Chain D 174–254（81 aa） Fragment：C-terminal ubiquitin-like domain, UNP residues 174-254	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；20 mg/mL protein and 3x cmc CHAPS in 20mM CAPS/NaOH pH10.5, 100mM NaCl, 5mM TCEP mixed 60-70% with 40-30% reservoir consisting of 0.1M HEPES/NaOH pH7.0, 10% PEG 5000 MME, 5% Tacsimate	Resolution 2.23 Å R-free 0.231
6REV Cryo-EM structure of the N-terminal DC repeat (NDC) of human doublecortin (DCX) bound to 13-protofilament GDP-microtubule Deposited 2019-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 44–142（99 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6RF2 Cryo-EM structure of the C-terminal DC repeat (CDC) of human doublecortin (DCX) bound to 13-protofilament GDP.Pi-microtubule Deposited 2019-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 178–264（87 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6RF8 Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule Deposited 2019-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 44–142（99 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6RFD Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 14-protofilament GDP-microtubule Deposited 2019-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 44–142（99 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

13 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCX_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–91； UniProt 251–341 Author chain E； PDBConstruct 1–91； UniProt 251–341

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	5ip4
Deposition date deposition_date	2016-03-09
Structure title title	X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN
Keywords keywords	DCX DOMAIN, UBIQUITIN-LIKE FOLD, MICROTUBULE ASSOCIATED, SIGNALING PROTEIN, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	27.04 Å
Radius of gyration Rg (electron density) rg_electron	26.39 Å
Forward intensity I(0) i0	29727900.00
Molecular weight molecular_weight	42362.0 kDa
Excluded volume excluded_volume	53142 Å³
Envelope volume envelope_volume	68639 Å³
Hydration-shell volume shell_volume	21657 Å³
Envelope diameter envelope_diameter	89.3 Å
Shell Rg shell_rg	33.32 Å
Envelope Rg envelope_rg	25.94 Å
Shape Rg shape_rg	26.35 Å
Total Rg total_rg	27.32 Å
Total atoms total_atoms	2986
Residues n_residues	383
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	84.5 Å
Rg (real space) rg_real	26.98 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	2.9730e+07
I(0) uncertainty (real space) i0_real_error	4.6690e+05
Rg (reciprocal space) rg_reciprocal	27.00 Å
I(0) (reciprocal space) i0_reciprocal	29730000.0000
Solution quality estimate total_estimate	0.8940
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.677
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9794000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.988

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	XA4551 NANOBODY AGAINST C-DCX
Molecular weight formula_weight	13419.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3373

QVQLQESGGGLVQAGGSLRLSCTASVNIIGGNHWAWYRQAPGQQRDLVASLSRYNANYADSVKGRFTISRDNAKNAAYLQMNSLKPEDTAIYFCALENYYWGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
通用名 common_name	LLAMA
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Neuronal migration protein doublecortin
Molecular weight formula_weight	10357.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

ARENKDFVRPKLVTIIRSGVKPRKAVRVLLNKKTAHSFEQVLTDITEAIKLETGVVKKLYTLDGKQVTCLHDFFGDDDVFIACGPEKFRYA

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	387

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5ip4a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5ip4a2
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

Domain ID domain_id	d5ip4b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5ip4b2
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 (4 domains)

Domain ID domain_id	5ip4A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ip4B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ip4D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	230 — Doublecortin domain

Domain ID domain_id	5ip4E00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	230 — Doublecortin domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	89.840 Å
Unit-cell length b length_b	86.191 Å
Unit-cell length c length_c	73.267 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	44.770 Å
R factor r_factor	0.1967
R_work r_work	0.1940
R_free r_free	0.2464

fit	/app/data/saxs_computation/ip/5ip4/5ip4.fit
pddf	/app/data/pr_computation/ip/5ip4/5ip4.pr.out
profile	/app/data/saxs_computation/ip/5ip4/5ip4.dat

X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN

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

Neuronal migration protein doublecortin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)