SAXSdb — 6r8m

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

NBS-LRR class disease resistance protein Pikh-1

Oryza sativa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	AVR-Pik protein × 1 （C4B8C2） (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	AVR-Pik protein × 1 （C4B8C2） (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D5L9G5_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–80； UniProt 186–263 Author chain B； PDBConstruct 3–80； UniProt 186–263 Author chain E； PDBConstruct 3–80； UniProt 186–263 Author chain F； PDBConstruct 3–80； UniProt 186–263

AVR-Pik protein

Magnaporthe oryzae

UniProt C4B8C2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	NBS-LRR class disease resistance protein Pikh-1 × 2 （D5L9G5） (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	NBS-LRR class disease resistance protein Pikh-1 × 2 （D5L9G5） (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C4B8C2_MAGOR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–92； UniProt 22–113 Author chain G； PDBConstruct 1–92； UniProt 22–113

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	6r8m
Deposition date deposition_date	2019-04-02
Structure title title	Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
Keywords keywords	NLR, Complex, HMA, Rice blast, PLANT PROTEIN; PLANT 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.

6r8m__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6r8m__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r8m__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.13 Å
Rg (electron density)	18.14 Å
Total Rg	19.12 Å
Atom count	1783
Residues	233
Excluded volume	32214 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r8m__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6r8m__assembly_2__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	NBS-LRR class disease resistance protein Pikh-1
Molecular weight formula_weight	8388.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	3916

GPGLKQKIVIKVAMEGNNCRSKAMALVASTGGVDSVALVGDLRDKIEVVGYGIDPIKLISALRKKVGDAELLQVSQAKED

Source Source

Source organism organism	Oryza sativa
Common name common_name	Rice
NCBI taxonomy ID ncbi_taxonomy_id	4530
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	AVR-Pik protein
Molecular weight formula_weight	10672.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

ETGNKYIEKRAIDLSRERDPNFFDNPGIPVPECFWFMFKNNVRQDAGTCYSSWKMDMKVGPNWVHIKSDDNCNLSGDFPPGWIVLGKKRPGF

Source Source

Source organism organism	Magnaporthe oryzae
NCBI taxonomy ID ncbi_taxonomy_id	318829
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	294

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6r8mA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	6r8mB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	6r8mE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	6r8mF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	66.456 Å
Unit-cell length b length_b	80.701 Å
Unit-cell length c length_c	105.577 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	16

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	29.500 Å
R factor r_factor	0.1886
R_work r_work	0.1864
R_free r_free	0.2301

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)

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

NBS-LRR class disease resistance protein Pikh-1

State in the Current Structure

Other States of the Same Protein in the Database

AVR-Pik protein

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

6r8m__assembly_2__model_1

6r8m__assembly_2__model_1 | I(q)

6r8m__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)

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

NBS-LRR class disease resistance protein Pikh-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

AVR-Pik protein

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

6r8m__assembly_2__model_1

6r8m__assembly_2__model_1 | I(q)

6r8m__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)