SAXSdb — 3afg

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

Subtilisin-like serine protease

Thermococcus kodakarensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5JIZ5_PYRKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–539； UniProt 24–562 Author chain B； PDBConstruct 1–539； UniProt 24–562

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	3afg
Deposition date deposition_date	2010-03-01
Structure title title	Crystal structure of ProN-Tk-SP from Thermococcus kodakaraensis
Keywords keywords	subtilisin, propeptide, Thermococcus kodakaraensis, Hydrolase, Protease, Serine protease; HYDROLASE
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.

3afg__assembly_1__model_1

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

Download this curve (.dat)

3afg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3afg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.62 Å
Rg (electron density)	23.69 Å
Total Rg	24.48 Å
Atom count	3782
Residues	505
Excluded volume	67243 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3afg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3afg__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Subtilisin-like serine protease
Molecular weight formula_weight	56905.2 kDa
EC 编号 ec_number	3.4.21.62
Mutation mutation	S359A
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	8255

APQKPAVRNVSQQKNYGLLTPGLFKKVQRMSWDQEVSTIIMFDNQADKEKAVEILDFLGAKIKYNYHIIPALAVKIKVKDLLIIAGLMDTGYFGNAQLSGVQFIQEDYVVKVAVETEGLDESAAQVMATNMWNLGYDGSGITIGIIDTGIDASHPDLQGKVIGWVDFVNGKTTPYDDNGHGTHVASIAAGTGAASNGKYKGMAPGAKLVGIKVLNGQGSGSISDIINGVDWAVQNKDKYGIKVINLSLGSSQSSDGTDSLSQAVNNAWDAGLVVVVAAGNSGPNKYTVGSPAAASKVITVGAVDKYDVITDFSSRGPTADNRLKPEVVAPGNWIIAARASGTSMGQPINDYYTAAPGTAMATPHVAGIAALLLQAHPSWTPDKVKTALIETADIVKPDEIADIAYGAGRVNAYKAAYYDNYAKLTFTGYVSNKGSQSHQFTISGAGFVTATLYWDNSGSDLDLYLYDPNGNQVDYSYTAYYGFEKVGYYNPTAGTWTIKVVSYSGSANYQVDVVSDGSLGQPSGGGSEPSPSPSPEPTV

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	311400
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	677

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3afgA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	80 — Peptidase S8 propeptide/proteinase inhibitor I9

Domain ID domain_id	3afgA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	200 — Peptidase S8/S53 domain

Domain ID domain_id	3afgA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	380 —

Domain ID domain_id	3afgB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	80 — Peptidase S8 propeptide/proteinase inhibitor I9

Domain ID domain_id	3afgB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	200 — Peptidase S8/S53 domain

Domain ID domain_id	3afgB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	380 —

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Unit-cell length a length_a	63.009 Å
Unit-cell length b length_b	123.996 Å
Unit-cell length c length_c	141.037 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	42.170 Å
R factor r_factor	0.1843
R_work r_work	0.1814
R_free r_free	0.2401

Crystal structure of ProN-Tk-SP from Thermococcus kodakaraensis

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

Subtilisin-like serine protease

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

3afg__assembly_1__model_1

3afg__assembly_1__model_1 | I(q)

3afg__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of ProN-Tk-SP from Thermococcus kodakaraensis

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

Subtilisin-like serine protease

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

3afg__assembly_1__model_1

3afg__assembly_1__model_1 | I(q)

3afg__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)