SAXSdb — 3q3j

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

Plexin-A2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1490–1600	Fragment：UNP residues 1490-1600	Rho-related GTP-binding protein Rho6 × 4 （Q92730） UNX UNKNOWN LIGAND × 36 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：vapor diffusion, sitting drops；pH 7.5；293 K；The complex sample (2.7 mg/mL) was incubated with 5mM Gpp(NH)p. Crystallization cocktail: 25.5% PEG3350, 0.2 M magnesium chloride, 0.1M Hepes. Seeding was applied in the production of the diffraction-quality crystal., pH 7.5, vapor diffusion, sitting drops, temperature 293K	Resolution 1.97 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PLXA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–112； UniProt 1490–1600

Rho-related GTP-binding protein Rho6

Homo sapiens

UniProt Q92730

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain B； UniProt 5–200	Fragment：UNP residues 5-200	Plexin-A2 × 4 （O75051） UNX UNKNOWN LIGAND × 36 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：vapor diffusion, sitting drops；pH 7.5；293 K；The complex sample (2.7 mg/mL) was incubated with 5mM Gpp(NH)p. Crystallization cocktail: 25.5% PEG3350, 0.2 M magnesium chloride, 0.1M Hepes. Seeding was applied in the production of the diffraction-quality crystal., pH 7.5, vapor diffusion, sitting drops, temperature 293K	Resolution 1.97 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3Q3J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CLS The crystal structure of the human RND1 GTPase in the active GTP bound state Deposited 2006-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–200（196 aa） Fragment：RESIDUES 5-200	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2M NAI, 20%(W/V)PEG3350, 0.1M BISTRISPROPANE PH8.5, 10% (V/V) ETHYLENE GLYCOL, 0.5% (V/V) DIMETHYLSULPHOXIDE, pH 8.50	Resolution 2.31 Å R-free 0.236
2CLS The crystal structure of the human RND1 GTPase in the active GTP bound state Deposited 2006-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 5–200（196 aa） Fragment：RESIDUES 5-200	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2M NAI, 20%(W/V)PEG3350, 0.1M BISTRISPROPANE PH8.5, 10% (V/V) ETHYLENE GLYCOL, 0.5% (V/V) DIMETHYLSULPHOXIDE, pH 8.50	Resolution 2.31 Å R-free 0.236
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 15 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 15 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 5–200（196 aa） Fragment：Residues 5-200 Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 30 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 5–200（196 aa） Fragment：Residues 5-200 Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 60 MG MAGNESIUM ION × 4 CA CALCIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
2REX Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 5–200（196 aa） Fragment：Residues 5-200 Chain D 5–200（196 aa） Fragment：Residues 5-200	Not recorded	UNX UNKNOWN LIGAND × 30 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248

2 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RND1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 19–214； UniProt 5–200

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	3q3j
Deposition date deposition_date	2010-12-21
Structure title title	Crystal structure of plexin A2 RBD in complex with Rnd1
Keywords keywords	Ras-binding domain, plexin, small gtpase, structural genomics consortium, SGC, Membrane protein-protein binding complex; Membrane protein/protein binding
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Plexin-A2
Molecular weight formula_weight	13007.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2153

GLIRQQIEYKTLILNCVNPDNENSPEIPVKVLNCDTITQVKEKILDAVYKNVPYSQRPRAVDMDLEWRQGRIARVVLQDEDITTKIEGDWKRLNTLMHYQVSDRSVVALVPK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Rho-related GTP-binding protein Rho6
Molecular weight formula_weight	24089.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHHHHHHSSGRENLYFQGRAPQPVVARCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCLNKPSPLPQKSPV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3q3ja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3q3jb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (2 domains)

Domain ID domain_id	3q3jA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3q3jB00
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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8. Citations (1)

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Unit-cell length a length_a	59.022 Å
Unit-cell length b length_b	67.129 Å
Unit-cell length c length_c	145.291 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.971 Å
Low-resolution limit resolution_low	39.276 Å
R factor r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2479

Crystal structure of plexin A2 RBD in complex with Rnd1

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

Plexin-A2

State in the Current Structure

Other States of the Same Protein in the Database

Rho-related GTP-binding protein Rho6

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (0)