› 5b4w

X-ray diffraction
2.6Å resolution

Crystal structure of Plexin inhibitor complex

Released:
DOI: 10.2210/pdb5b4w/pdb
PDB entry 5b4w coloured by chain, front view.
PDB entry 5b4w coloured by chain, side view.
PDB entry 5b4w coloured by chain, top view.
Source organisms:
Primary publication:
Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide.
Matsunaga Y, Bashiruddin NK, Kitago Y, Takagi J, Suga H
Cell Chem Biol 23 1341-1350 (2016)
PMID: 27984026

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128846 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Plexin-B1 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 579 amino acids
Theoretical weight: 61.93 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43157 (Residues: 8-535; Coverage: 24%)
Gene names: KIAA0407, PLXN5, PLXNB1, SEP
Sequence domains:
Structure domains:
Synthesized cyclic peptide Chains: G, H, I, J, K, L
Molecule details ›
Chains: G, H, I, J, K, L
Length: 18 amino acids
Theoretical weight: 2.02 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NAG 7 x NAG
1 modified residue:
Ligand DTR 6 x DTR

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P21
Unit cell:
a: 92.426Å b: 217.924Å c: 106.475Å
α: 90° β: 115.3° γ: 90°
R-values:
R R work R free
0.227 0.224 0.265
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

10 review citations

Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads.
Obexer et al. (2017)
9 more

3 mentions without citation

Structural Features and Binding Modes of Thioether-Cyclized Peptide Ligands.
Otero-Ramirez et al. (2018)
2 more