SAXSdb — 3kuq

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

Rho GTPase-activating protein 7

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1066–1275	Fragment：Rho-GAP domain	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；291 K；30% PEG-3350, 0.2M sodium chloride, 5% glycerol, 0.02M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.260

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 3KUQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DKY Solution structure of the SAM-domain of Rho-GTPase-activating protein 7 Deposited 2006-04-14	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–78（78 aa） Fragment：SAM-domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure AMBIENT NMR sample composition 1.08mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2GYT Solution structure of the SAM (sterile alpha motif) domain of DLC1 (deleted in liver cancer 1) Deposited 2006-05-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa） Fragment：sterile alpha motif (SAM) domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR sample composition 1mM DLC1-SAM 15N, 13C-labaled; 50mM sodium phosphate buffer(pH 7.0); 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM DLC1-SAM 15N-labaled; 50mM sodium phosphate buffer(pH 7.0); 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KAP Solution structure of DLC1-SAM Deposited 2008-11-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–76（60 aa） Fragment：sterile alpha motif (SAM) domain, UNP residues 17-76	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR sample composition 1mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM [U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100 % D2O, 100% D2O \| 100% D2O NMR sample composition 1mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100% D2O, 100% D2O \| 100% D2O	Resolution not provided
2LOZ The novel binding mode of DLC1 and Tensin2 PTB domain Deposited 2012-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 811–824（14 aa） Fragment：UNP residues 811-824	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O \| 100% D2O NMR sample composition 1.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O \| 100% D2O	Resolution not provided
5FZT The crystal structure of R7R8 in complex with a DLC1 fragment. Deposited 2016-03-15	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 467–489（23 aa） Fragment：TBS, UNP RESIDUES 467-489	Not recorded	MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；15% ETHANOL, 0.1 M TRIS PH 7.4 AT 4OC	Resolution 2.10 Å R-free 0.231

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RHG07_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–228； UniProt 1066–1275

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	3kuq
Deposition date deposition_date	2009-11-27
Structure title title	Crystal structure of the DLC1 RhoGAP domain
Keywords keywords	;Structural Genomics Consortium, GTPase activation, SGC, Alternative splicing, Cytoplasm, Phosphoprotein, Polymorphism, HYDROLASE ACTIVATOR ;; HYDROLASE ACTIVATOR
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 (3)

Entity 1 Entity 1 polymer

Description description	Rho GTPase-activating protein 7
Molecular weight formula_weight	26038.9 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	1542

MHHHHHHSSGRENLYFQGSVFGVPLTVNVQRTGQPLPQSIQQAMRYLRNHCLDQVGLFRKSGVKSRIQALRQMNEGAIDCVNYEGQSAYDVADMLKQYFRDLPEPLMTNKLSETFLQIYQYVPKDQRLQAIKAAIMLLPDENREVLQTLLYFLSDVTAAVKENQMTPTNLAVCLAPSLFHLNTLKRENSSPRVMQRKQSLGKPDQKDLNENLAATQGLAHMIAECKKL

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 non-polymer

Description description	UNKNOWN ATOM OR ION
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	30

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3kuqA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

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8. Citations (1)

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Unit-cell length a length_a	60.577 Å
Unit-cell length b length_b	97.502 Å
Unit-cell length c length_c	92.577 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.750 Å
R factor r_factor	0.2182
R_work r_work	0.2162
R_free r_free	0.2603

Crystal structure of the DLC1 RhoGAP domain