SAXSdb — 6nid

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

Peripheral plasma membrane protein CASK

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Neurexin-1 × 1 （Q9ULB1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Neurexin-1 × 1 （Q9ULB1） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Neurexin-1 × 1 （Q9ULB1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSKP_HUMAN
Isoform	O14936-5
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–88； UniProt 102–187 Author chain B； PDBConstruct 3–88； UniProt 102–187 Author chain C； PDBConstruct 3–88； UniProt 102–187

Neurexin-1

OrganismNot specified

UniProt Q9ULB1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peripheral plasma membrane protein CASK × 1 （O14936） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peripheral plasma membrane protein CASK × 1 （O14936） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Peripheral plasma membrane protein CASK × 1 （O14936） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NRX1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–10； UniProt 1468–1477 Author chain E； PDBConstruct 1–10； UniProt 1468–1477 Author chain F； PDBConstruct 1–10； UniProt 1468–1477

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	6nid
Deposition date deposition_date	2018-12-27
Structure title title	Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide
Keywords keywords	;PDZ domain, MAGUK protein family, peripheral plasma membrane protein, protein binding, c-terminal peptide binding, Neurexin, protein binding-peptide complex ;; protein binding/peptide
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6nid__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6nid__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nid__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	13.93 Å
Rg (electron density)	12.25 Å
Total Rg	13.59 Å
Atom count	718
Residues	91
Excluded volume	12810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nid__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nid__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6nid__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Peripheral plasma membrane protein CASK
Molecular weight formula_weight	10118.9 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2472

MGRVRLVQFQKNTDEPMGITLKMNELNHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Neurexin-1
Molecular weight formula_weight	1318.5 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

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

KKNKDKEYYV

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6nidA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	6nidB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	6nidC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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Unit-cell length a length_a	36.328 Å
Unit-cell length b length_b	51.177 Å
Unit-cell length c length_c	72.412 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	41.666 Å
R factor r_factor	0.1942
R_work r_work	0.1918
R_free r_free	0.2396

Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide

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

Peripheral plasma membrane protein CASK

State in the Current Structure

Other States of the Same Protein in the Database

Neurexin-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6nid__assembly_3__model_1

6nid__assembly_3__model_1 | I(q)

6nid__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide

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

Peripheral plasma membrane protein CASK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Neurexin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6nid__assembly_3__model_1

6nid__assembly_3__model_1 | I(q)

6nid__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)