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Crystal structure of the cytoplasmic domain of human plexin B1
Analyse Crystal structure of the cytoplasmic domain of human plexin B1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HM6
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-B1; Unknown peptide
- UniProt
- O43157
- Ligands
- UNX
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Plexin-B1 | protein | 503 | 58% helix, 9% strand | O43157 |
| C | Unknown peptide | protein | 27 | 89% helix, 0% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 19 copies · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.69 | 0.79 | 60 | empty |
| 2 | 170 | 0.44 | 0.74 | 38 | UNX |
| 3 | 95 | 0.40 | 0.77 | 17 | UNX |
| 4 | 90 | 0.39 | 0.76 | 24 | empty |
| 5 | 62 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- X–C · 420 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O43157
- Elsewhere: RCSB PDB 3HM6 · PDBe 3HM6 · UniProt O43157
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