SAXSdb — 4typ

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

Adenylate kinase

Bacillus subtilis 168

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 ZINC ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 ZINC ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAD_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 1–217 Author chain B； PDBConstruct 1–217； UniProt 1–217 Author chain C； PDBConstruct 1–217； UniProt 1–217 Author chain D； PDBConstruct 1–217； UniProt 1–217

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	4typ
Deposition date deposition_date	2014-07-09
Structure title title	Crystal structure of an adenylate kinase mutant--AKm1
Keywords keywords	adenylate kinase, ATP binding, TRANSFERASE; TRANSFERASE
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.

4typ__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4typ__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4typ__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	17.02 Å
Rg (electron density)	16.16 Å
Total Rg	17.10 Å
Atom count	1542
Residues	186
Excluded volume	27354 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4typ__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4typ__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4typ__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4typ__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Adenylate kinase
Molecular weight formula_weight	24456.2 kDa
EC 编号 ec_number	2.7.4.3
Mutation mutation	;L3I, G17A, R19K, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, Y109H, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180K, D184A, S187D, E188S, G190E, Y191V, A193R, Q198E, I201M, Q202E, D203K, Y205F, A206K, V208L, K209R, D210E, G213Q, K216A, K217R ;
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,B,A,D
Atom count atom_count	6504

MNIVLMGLPGAGKGTQAEKIVAKYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVRERLSKSDCERGFLLDGFPRTVAQAEALEEILEEMGRKLEHVIHIDVRQEELMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVAKRLEVNMKQMKPLLAFYDSKEVLRNVNGEQDMEKVFKDLRELLQGLAR

Source Source

Source organism organism	Bacillus subtilis 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
Molecular weight formula_weight	916.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4typA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4typB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4typC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4typD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	43.641 Å
Unit-cell length b length_b	123.338 Å
Unit-cell length c length_c	86.693 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2898
R_work r_work	0.2875
R_free r_free	0.3288

Crystal structure of an adenylate kinase mutant--AKm1

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

Adenylate kinase

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

4typ__assembly_4__model_1

4typ__assembly_4__model_1 | I(q)

4typ__assembly_4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of an adenylate kinase mutant--AKm1

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

Adenylate kinase

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

4typ__assembly_4__model_1

4typ__assembly_4__model_1 | I(q)

4typ__assembly_4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)