5ikc

X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB

Method: X-RAY DIFFRACTION D_max: 125.6 Å Quality: GOOD

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

MAb 6H10 light chain

Mus musculus

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 22–233	Not recorded	Ighg protein × 1 （Q569X1） Neuronal migration protein doublecortin × 1 （O43602） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain L； UniProt 22–233	Not recorded	Ighg protein × 1 （Q569X1） Neuronal migration protein doublecortin × 1 （O43602） 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

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 5IKC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VLP PCSK9 complex with LDLR antagonist peptide and Fab7G7 Deposited 2017-04-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–234（108 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；ammonium acetate, 1,8diaminooctane	Resolution 2.90 Å R-free 0.209
6U2F PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2 Deposited 2019-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–234（108 aa） Fragment：Fab	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane	Resolution 2.94 Å R-free 0.209
6U3I Design of organo-peptides as bipartite PCSK9 antagonists Deposited 2019-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–234（108 aa） Fragment：Fab	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane	Resolution 2.90 Å R-free 0.217
6VRH Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine and 8B6 Fab Deposited 2020-02-07	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 117–234（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 8PR Paroxetine × 1 CL CHLORIDE ION × 1 LMT DODECYL-BETA-D-MALTOSIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6VRK Cryo-EM structure of the wild-type human serotonin transporter complexed with Br-paroxetine and 8B6 Fab Deposited 2020-02-07	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 117–234（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LMT DODECYL-BETA-D-MALTOSIDE × 1 RFS Br-paroxetine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6VRL Cryo-EM structure of the wild-type human serotonin transporter complexed with I-paroxetine and 8B6 Fab Deposited 2020-02-07	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 117–234（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LMT DODECYL-BETA-D-MALTOSIDE × 1 RFY I-paroxetine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0U5BC76_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–213； UniProt 22–233 Author chain L； PDBConstruct 2–213； UniProt 22–233

Ighg protein

Mus musculus

UniProt Q569X1

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 B； UniProt 21–240	Non-standard monomer：Yes (specific site not provided by mmCIF)	MAb 6H10 light chain × 1 （A0A0U5BC76） Neuronal migration protein doublecortin × 1 （O43602） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain H； UniProt 21–240	Non-standard monomer：Yes (specific site not provided by mmCIF)	MAb 6H10 light chain × 1 （A0A0U5BC76） Neuronal migration protein doublecortin × 1 （O43602） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5IKC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VXR The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423) Deposited 2017-05-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 141–239（99 aa）	Not recorded	GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；12.5% PEG3000, 100 mM sodium chloride, 100 mM sodium phosphate dibasic/citric acid, pH 6.2	Resolution 1.40 Å R-free 0.190
6U2F PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2 Deposited 2019-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 137–239（103 aa） Fragment：Fab	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane	Resolution 2.94 Å R-free 0.209

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q569X1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–215； UniProt 21–240 Author chain H； PDBConstruct 2–215； UniProt 21–240

Neuronal migration protein doublecortin

Homo sapiens

UniProt O43602

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 M； UniProt 52–140	Fragment：N-terminal domain, UNP Residues 133-221	MAb 6H10 light chain × 1 （A0A0U5BC76） Ighg protein × 1 （Q569X1） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain N； UniProt 52–140	Fragment：N-terminal domain, UNP Residues 133-221	MAb 6H10 light chain × 1 （A0A0U5BC76） Ighg protein × 1 （Q569X1） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5IKC	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 ligand/ion 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 ligand/ion 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
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
5IP4 X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-09	Different construct 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 251–341（91 aa） Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 251-341	Not recorded	No recorded non-water small molecule	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
5IP4 X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN Deposited 2016-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 251–341（91 aa） Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 251-341	Not recorded	No recorded non-water small molecule	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
6FNZ Crystal Structure of domain-swapped C-terminal domain of human doublecortin Deposited 2018-02-05	Different construct Different mutation/modification Different ligand/ion 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 ligand/ion 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	3
Chains and sequence ranges	Author chain M； PDBConstruct 2–90； UniProt 52–140 Author chain N； PDBConstruct 2–90； UniProt 52–140

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ikc
Deposition date deposition_date	2016-03-03
Structure title title	X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB
Keywords keywords	DCX DOMAIN, UBIQUITIN-LIKE FOLD, MICROTUBULE ASSOCIATED, SIGNALING PROTEIN, TRANSFERASE; TRANSFERASE
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	36.44 Å
Radius of gyration Rg (electron density) rg_electron	36.06 Å
Forward intensity I(0) i0	204256000.00
Molecular weight molecular_weight	112570.0 kDa
Excluded volume excluded_volume	139720 Å³
Envelope volume envelope_volume	184890 Å³
Hydration-shell volume shell_volume	44118 Å³
Envelope diameter envelope_diameter	133.6 Å
Shell Rg shell_rg	40.88 Å
Envelope Rg envelope_rg	35.72 Å
Shape Rg shape_rg	36.05 Å
Total Rg total_rg	36.43 Å
Total atoms total_atoms	7923
Residues n_residues	1027
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	125.6 Å
Rg (real space) rg_real	36.52 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	2.0430e+08
I(0) uncertainty (real space) i0_real_error	3.4890e+06
Rg (reciprocal space) rg_reciprocal	36.47 Å
I(0) (reciprocal space) i0_reciprocal	204200000.0000
Solution quality estimate total_estimate	0.8709
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.9 Å
Skewness Skewness skewness	0.396
Kurtosis Kurtosis kurtosis	-0.227
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20260000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.848

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MAb 6H10 light chain
Molecular weight formula_weight	23510.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	8308

DIVMTQSQKLMSTSVGDRVSITCKASQIVDTAVAWYQQKPGQSPKPLIYLASNRHTGVPDRFTGSGSGTDFTLTINNVQSDDLADYFCLQHWNYPLTFGAGTKLELKGADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ighg protein
Molecular weight formula_weight	22799.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H

QVQLQQSGADLVRPGASVKLSCTASGFDIKDDYVHWVKQRPEQGLEWIGRIDPANGATKYAPKFQDKATLTADTSSNTAYLQLSSLTSEDTAVYYCGRSKYFDSWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Neuronal migration protein doublecortin
Molecular weight formula_weight	10398.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

AAKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRYIYTIDGSRKIGSMDELEEGESYVCSSDNFFKKVEYTK

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 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	385

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d5ikca1
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.1.1.0 — automated matches

Domain ID domain_id	d5ikca2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5ikca3
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	d5ikcb1
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	d5ikcb2
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	d5ikch1
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	d5ikch2
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	d5ikcl1
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.1.1.0 — automated matches

Domain ID domain_id	d5ikcl2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5ikcl3
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	d5ikcm1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.11 — Doublecortin (DC)
Family Family family	d.15.11.1 — Doublecortin (DC)

Domain ID domain_id	d5ikcm2
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	d5ikcn1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.11 — Doublecortin (DC)
Family Family family	d.15.11.1 — Doublecortin (DC)

Domain ID domain_id	d5ikcn2
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 (10 domains)

Domain ID domain_id	5ikcA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ikcM00
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	5ikcN00
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	66.858 Å
Unit-cell length b length_b	110.399 Å
Unit-cell length c length_c	75.092 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.060 Å
Low-resolution limit resolution_low	41.825 Å
R factor r_factor	0.2011
R_work r_work	0.1978
R_free r_free	0.2653

X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB

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

MAb 6H10 light chain

State in the Current Structure

Other States of the Same Protein in the Database

Ighg protein

State in the Current Structure

Other States of the Same Protein in the Database

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (14 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ik/5ikc/5ikc.fit
pddf	/app/data/pr_computation/ik/5ikc/5ikc.pr.out
profile	/app/data/saxs_computation/ik/5ikc/5ikc.dat