SAXSdb — 2ki6

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

Synaptotagmin-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Heparin-binding growth factor 1 × 2 （P05230） Protein S100-A13 × 1 （Q99584） Protein S100-A13 × 1 （Q99584）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 141–268 Author chain F； PDBConstruct 1–128； UniProt 141–268

Heparin-binding growth factor 1

Homo sapiens

UniProt P05230

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Synaptotagmin-1 × 2 （P21579） Protein S100-A13 × 1 （Q99584） Protein S100-A13 × 1 （Q99584）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FGF1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–133； UniProt 23–155 Author chain E； PDBConstruct 1–133； UniProt 23–155

Protein S100-A13

Homo sapiens

UniProt Q99584

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Synaptotagmin-1 × 2 （P21579） Heparin-binding growth factor 1 × 2 （P05230）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S10AD_HUMAN
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 1–98； UniProt 1–98 Author chain D； PDBConstruct 1–98； UniProt 1–98

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	2ki6
Deposition date deposition_date	2009-04-28
Structure title title	The FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion
Keywords keywords	;FGF1-S100A13-C2A hetero-hexameric complex, FGF1, S100A13, C2A, Calcium, Cell junction, Cytoplasmic vesicle, Glycoprotein, Lipoprotein, Membrane, Metal-binding, Palmitate, Phosphoprotein, Synapse, Transmembrane, Acetylation, Alternative splicing, Angiogenesis, Developmental protein, Differentiation, Growth factor, Heparin-binding, Mitogen, Polymorphism, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
Experimental Method method	SOLUTION NMR

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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.

2ki6__assembly_1__model_9

Assembly 1 · Model 9 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ki6__assembly_1__model_9 | I(q)

100 plotted points; both axes use logarithmic scales.

2ki6__assembly_1__model_9 | P(r) · Pending

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

Rg（Guinier）	31.75 Å
Rg (electron density)	30.81 Å
Total Rg	31.56 Å
Atom count	11675
Residues	715
Excluded volume	104170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ki6__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2ki6__assembly_1__model_2`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2ki6__assembly_1__model_3`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2ki6__assembly_1__model_4`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2ki6__assembly_1__model_5`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2ki6__assembly_1__model_6`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2ki6__assembly_1__model_7`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2ki6__assembly_1__model_8`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2ki6__assembly_1__model_9`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2ki6__assembly_1__model_10`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2ki6__assembly_1__model_11`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2ki6__assembly_1__model_12`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2ki6__assembly_1__model_13`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2ki6__assembly_1__model_14`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2ki6__assembly_1__model_15`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2ki6__assembly_1__model_16`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`2ki6__assembly_1__model_17`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`2ki6__assembly_1__model_18`	hexameric （6）	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	Synaptotagmin-1
Molecular weight formula_weight	14783.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	210150

EKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEK

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 2 Entity 2 polymer

Description description	Heparin-binding growth factor 1
Molecular weight formula_weight	15118.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

YKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPNEECLFLERLEENHYNTYISKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVSSD

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 3 Entity 3 polymer

Description description	Protein S100-A13
Molecular weight formula_weight	11488.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK

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	Protein S100-A13
Molecular weight formula_weight	11489.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK

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)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2ki6a_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

Domain ID domain_id	d2ki6b_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.1 — Cytokine
Family Family family	b.42.1.1 — Fibroblast growth factors (FGF)

Domain ID domain_id	d2ki6c_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

Domain ID domain_id	d2ki6d_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

Domain ID domain_id	d2ki6e_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.1 — Cytokine
Family Family family	b.42.1.1 — Fibroblast growth factors (FGF)

Domain ID domain_id	d2ki6f_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.2 — Synaptotagmin-like (S variant)

CATH v4.4 (6 domains)

Domain ID domain_id	2ki6A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	2ki6B00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ki6C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2ki6D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2ki6E00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ki6F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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The FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion

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

Synaptotagmin-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

Heparin-binding growth factor 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

Protein S100-A13

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

2ki6__assembly_1__model_9

2ki6__assembly_1__model_9 | I(q)

2ki6__assembly_1__model_9 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (4)

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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)