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2rex

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Plexin-B1

Homo sapiens

UniProt O43157

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1743–1862 Fragment：Residues 1743-1862 Rho-related GTP-binding protein Rho6 × 1 （Q92730） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1743–1862 Fragment：Residues 1743-1862 Rho-related GTP-binding protein Rho6 × 1 （Q92730） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1743–1862 Chain C； UniProt 1743–1862 Fragment：Residues 1743-1862 Rho-related GTP-binding protein Rho6 × 2 （Q92730） 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
4 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1743–1862 Chain C； UniProt 1743–1862 Fragment：Residues 1743-1862 Rho-related GTP-binding protein Rho6 × 4 （Q92730） 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
5 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1743–1862 Chain C； UniProt 1743–1862 Fragment：Residues 1743-1862 Rho-related GTP-binding protein Rho6 × 2 （Q92730） 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

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 2REX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2JPH NMR solution structure of the Rho GTPase binding domain of human plexin-b1 Deposited 2007-05-11 Different construct Different mutation/modification Different oligomeric state 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 1743–1862（120 aa） Fragment：Sequence database residues 1743-1862
Mutation：W1830F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 1.75 mM [U-100% 13C; U-100% 15N] protein, 90%H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM [U-100% 13C; U-100% 15N; 80% 2H] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2OS6 Solution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1 Deposited 2007-02-05 Different construct 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 2128–2135（8 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 50 mM phosphate buffer, 50mM NaCl；Pressure 1
NMR sample composition 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 90% H2O, 10% D2O | 50mM phosphate buffer, 90% H2O, 10% D2O
NMR sample composition 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 99.9% D2O | 50mM phosphate buffer, 99.9% D2O
Resolution not provided
2R2O Crystal structure of the effector domain of human Plexin B1 Deposited 2007-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1743–1862（120 aa） Fragment：Effector domain: Residues 1743-1862
Chain B 1743–1862（120 aa） Fragment：Effector domain: Residues 1743-1862
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；291 K；2.6M Sodium chloride, 18% Ethylene glycol, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.00 Å R-free 0.269
3HM6 Crystal structure of the cytoplasmic domain of human plexin B1 Deposited 2009-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1511–2135（625 aa） Fragment：Cytoplasmic domain (UNP residues 1511-2135)
Mutation：S1625T UNX UNKNOWN LIGAND × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；16% peg-2000 mme, 0.1M TRIS, 0.2M TMAO, pH 8, vapor diffusion, hanging drop, temperature 291K
Resolution 2.40 Å R-free 0.262
3OL2 Receptor-ligand structure of Human Semaphorin 4D with Plexin B1. Deposited 2010-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 20–535（516 aa） Fragment：Extracellular domainsl (1-2)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.1 M Tris,0.2 M calcium acetate, 6% v/v glycerol, 20% PEG3000, pH 7, VAPOR DIFFUSION, temperature 294K
Resolution 2.99 Å R-free 0.237
3SU8 Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1533–2135（603 aa） Fragment：UNP residues 1533-2135
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.238
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1511–2135（625 aa） Fragment：UNP residues 1533-2135
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.39 Å R-free 0.264
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1511–2135（625 aa） Fragment：UNP residues 1533-2135
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.39 Å R-free 0.264
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1511–2135（625 aa） Fragment：UNP residues 1533-2135
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.39 Å R-free 0.264
3SUA Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 Deposited 2011-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1511–2135（625 aa） Fragment：UNP residues 1533-2135
Chain E 1511–2135（625 aa） Fragment：UNP residues 1533-2135
Chain F 1511–2135（625 aa） Fragment：UNP residues 1533-2135
Not recorded MG MAGNESIUM ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.39 Å R-free 0.264
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–535（516 aa） Fragment：UNP residues 20-535
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000
Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–535（516 aa） Fragment：UNP residues 20-535
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000
Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–535（516 aa） Fragment：UNP residues 20-535
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000
Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 20–535（516 aa） Fragment：UNP residues 20-535
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000
Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 20–535（516 aa） Fragment：UNP residues 20-535
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000
Resolution 2.60 Å R-free 0.265
5B4W Crystal structure of Plexin inhibitor complex Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 20–535（516 aa） Fragment：UNP residues 20-535
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M tri-sodium citrate, 13% PEG 8000
Resolution 2.60 Å R-free 0.265
7VF3 Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide Deposited 2021-09-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–535（517 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M sodium acetate buffer, 20% PEG 400, 0.2M Calcium acetate
Resolution 2.29 Å R-free 0.226
7VF3 Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide Deposited 2021-09-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–535（517 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M sodium acetate buffer, 20% PEG 400, 0.2M Calcium acetate
Resolution 2.29 Å R-free 0.226
7VG7 Plexin B1 extracellular fragment in complex with lasso-grafted PB1m6A9 peptide Deposited 2021-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–535（517 aa）
Mutation：T19S PGE TRIETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES or HEPES, 14-16% PEG 3350
Resolution 2.50 Å R-free 0.243
8B3K Crystal structure of human Plexin-B1 (20-535) in the unbound state Deposited 2022-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–535（516 aa）
Chain B 20–535（516 aa）
Not recorded CD CADMIUM ION × 14 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；1.0 M sodium acetate, 0.2 M cadmium sulphate, 0.1 M HEPES, pH 7.5
Resolution 2.69 Å R-free 0.245

11 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLXB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–121； UniProt 1743–1862 Author chain C； PDBConstruct 2–121； UniProt 1743–1862

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 5–200 Fragment：Residues 5-200 Plexin-B1 × 1 （O43157） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 5–200 Fragment：Residues 5-200 Plexin-B1 × 1 （O43157） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 5–200 Chain D； UniProt 5–200 Fragment：Residues 5-200 Plexin-B1 × 2 （O43157） 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
4 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 5–200 Chain D； UniProt 5–200 Fragment：Residues 5-200 Plexin-B1 × 4 （O43157） 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
5 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 5–200 Chain D； UniProt 5–200 Fragment：Residues 5-200 Plexin-B1 × 2 （O43157） 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

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 2REX 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
3Q3J Crystal structure of plexin A2 RBD in complex with Rnd1 Deposited 2010-12-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 5–200（196 aa） Fragment：UNP residues 5-200
Not recorded 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

2 other PDB entries and 3 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 2–197； UniProt 5–200 Author chain D； PDBConstruct 2–197； 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.

SAXS scattering curve SAXS Profile

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2rex
Deposition date deposition_date2007-09-27
Structure title titleCrystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase
Keywords keywords;complex, Structural Genomics Consortium, SGC, gtpase, gnp, Plexin, effector domain, Glycoprotein, Membrane, Phosphorylation, Receptor, Secreted, Transmembrane, Cytoskeleton, GTP-binding, Lipoprotein, Methylation, Nucleotide-binding, Prenylation, SIGNALING PROTEIN-LIPOPROTEIN COMPLEX ;; SIGNALING PROTEIN/LIPOPROTEIN
Experimental Method methodX-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 (7)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2rexa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.10 — Rho GTPase binding domain
Domain ID domain_idd2rexb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd2rexc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.10 — Rho GTPase binding domain
Domain ID domain_idd2rexd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (4 domains)

Domain ID domain_id2rexA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2rexB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2rexC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2rexD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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