SAXSdb — 1kil

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

Synaptobrevin SNARE motif

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Syntaxin SNARE motif short × 1 （P32851） SNAP-25 N-terminal SNARE motif × 1 （P60880） SNAP-25 C-terminal SNARE motif × 1 （P60880） Complexin I SNARE-complex binding region × 1 （P63041） MAGNESIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAMP2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–66； UniProt 28–92

Syntaxin SNARE motif short

Rattus norvegicus

UniProt P32851

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Synaptobrevin SNARE motif × 1 （P63045） SNAP-25 N-terminal SNARE motif × 1 （P60880） SNAP-25 C-terminal SNARE motif × 1 （P60880） Complexin I SNARE-complex binding region × 1 （P63041） MAGNESIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STX1A_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–62； UniProt 192–250

SNAP-25 N-terminal SNARE motif

Homo sapiens

UniProt P60880

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Synaptobrevin SNARE motif × 1 （P63045） Syntaxin SNARE motif short × 1 （P32851） Complexin I SNARE-complex binding region × 1 （P63041） MAGNESIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SN25_HUMAN
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 2–73； UniProt 10–81 Author chain D； PDBConstruct 1–66； UniProt 139–204

Complexin I SNARE-complex binding region

Rattus norvegicus

UniProt P63041

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Synaptobrevin SNARE motif × 1 （P63045） Syntaxin SNARE motif short × 1 （P32851） SNAP-25 N-terminal SNARE motif × 1 （P60880） SNAP-25 C-terminal SNARE motif × 1 （P60880） MAGNESIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPLX1_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 9–49； UniProt 32–72

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	1kil
Deposition date deposition_date	2001-12-03
Structure title title	Three-dimensional structure of the complexin/SNARE complex
Keywords keywords	Helix bound to four helix bundle, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

1kil__assembly_1__model_1

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

Download this curve (.dat)

1kil__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kil__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.34 Å
Rg (electron density)	29.12 Å
Total Rg	29.19 Å
Atom count	2478
Residues	303
Excluded volume	43285 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kil__assembly_1__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	Synaptobrevin SNARE motif
Molecular weight formula_weight	7660.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2610

GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKN

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Syntaxin SNARE motif short
Molecular weight formula_weight	7192.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSD

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	SNAP-25 N-terminal SNARE motif
Molecular weight formula_weight	8642.6 kDa
Mutation mutation	W added at C-terminus
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSLEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLW

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 BL21(DE3)

Entity 4 Entity 4 polymer

Description description	SNAP-25 C-terminal SNARE motif
Molecular weight formula_weight	7613.5 kDa
Mutation mutation	W added at C-terminus
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLW

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 BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Complexin I SNARE-complex binding region
Molecular weight formula_weight	5766.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GSKDPDAAKKEEERQEALRQAEEERKAKYAKMEAEREVMRQGIRDKYGI

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1kila_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d1kilb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d1kilc_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d1kild_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d1kile_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

CATH v4.4 (5 domains)

Domain ID domain_id	1kilA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1kilB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1kilC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1kilD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1kilE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	580 — Single Helix bin

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Unit-cell length a length_a	40.489 Å
Unit-cell length b length_b	60.425 Å
Unit-cell length c length_c	159.787 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	2.300 Å
Low-resolution limit resolution_low	32.230 Å
R factor r_factor	—
R_work r_work	0.2450
R_free r_free	0.3050

Three-dimensional structure of the complexin/SNARE complex

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

Synaptobrevin SNARE motif

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Syntaxin SNARE motif short

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SNAP-25 N-terminal SNARE motif

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Complexin I SNARE-complex binding region

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

1kil__assembly_1__model_1

1kil__assembly_1__model_1 | I(q)

1kil__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)