Plexin-B1
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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain X； UniProt 1511–2135 | Fragment：Cytoplasmic domain (UNP residues 1511-2135) Mutation：S1625T | Unknown peptide × 1 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 |
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 3HM6 | 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 mutation/modification 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 |
| 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 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1743–1862（120 aa）
Fragment：Residues 1743-1862
|
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 ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1743–1862（120 aa）
Fragment：Residues 1743-1862
|
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 A
1743–1862（120 aa）
Fragment：Residues 1743-1862
Chain C
1743–1862（120 aa）
Fragment：Residues 1743-1862
|
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1743–1862（120 aa）
Fragment：Residues 1743-1862
Chain C
1743–1862（120 aa）
Fragment：Residues 1743-1862
|
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 A
1743–1862（120 aa）
Fragment：Residues 1743-1862
Chain C
1743–1862（120 aa）
Fragment：Residues 1743-1862
|
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 |
| 3OL2 Receptor-ligand structure of Human Semaphorin 4D with Plexin B1. Deposited 2010-08-25 | Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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）
|
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 mutation/modification 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 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
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 24 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 X； PDBConstruct 20–644； UniProt 1511–2135 |