SAXSdb — 3ni6

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

70 kDa peptidylprolyl isomerase

Plasmodium vivax

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5K8X6_PLAVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 1–126 Author chain B； PDBConstruct 1–126； UniProt 1–126

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	3ni6
Deposition date deposition_date	2010-06-15
Structure title title	Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35
Keywords keywords	FK506 binding domain, ISOMERASE; ISOMERASE
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.

3ni6__assembly_1__model_1

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

Download this curve (.dat)

3ni6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ni6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.26 Å
Rg (electron density)	19.17 Å
Total Rg	20.16 Å
Atom count	1945
Residues	245
Excluded volume	34485 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ni6__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	70 kDa peptidylprolyl isomerase
Molecular weight formula_weight	13971.7 kDa
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	2273

MEQETLEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGYGEEGCGESIPGNSVLIFEIELISFRE

Source Source

Source organism organism	Plasmodium vivax
NCBI taxonomy ID ncbi_taxonomy_id	5855
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	278

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ni6a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.0 — automated matches

Domain ID domain_id	d3ni6b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3ni6A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3ni6B01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	54.917 Å
Unit-cell length b length_b	41.857 Å
Unit-cell length c length_c	55.339 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.420 Å
Low-resolution limit resolution_low	22.670 Å
R factor r_factor	0.1731
R_work r_work	0.1707
R_free r_free	0.2187

Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35

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

70 kDa peptidylprolyl isomerase

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

3ni6__assembly_1__model_1

3ni6__assembly_1__model_1 | I(q)

3ni6__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35

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

70 kDa peptidylprolyl isomerase

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

3ni6__assembly_1__model_1

3ni6__assembly_1__model_1 | I(q)

3ni6__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)