Research workbench
Plexin B1 extracellular fragment in complex with lasso-grafted PB1M7 peptide
Analyse Plexin B1 extracellular fragment in complex with lasso-grafted PB1M7 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VF3
- Type
- protein
- Length
- 1,018 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-B1; UTEROGLOBIN,PB1M7 PEPTIDE,UTEROGLOBIN
- UniProt
- O43157, P11684
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-B1 | protein | 494 | 11% helix, 39% strand | O43157 |
| B, D | UTEROGLOBIN,PB1M7 PEPTIDE,UTEROGLOBIN | protein | 15 | 47% helix, 0% strand | P11684 |
| C | Plexin-B1 | protein | 494 | 9% helix, 41% strand | O43157 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.75 | 0.80 | 48 | empty |
| 2 | 660 | 0.72 | 0.79 | 47 | PEG |
| 3 | 120 | 0.65 | 0.89 | 29 | empty |
| 4 | 119 | 0.61 | 0.87 | 29 | empty |
| 5 | 343 | 0.59 | 0.77 | 55 | PG4 |
Interfaces
3 interfaces between chains.
- C–D · 1014 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 976 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7VF3 · Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O43157 · AlphaFold monomer V2.0 prediction for plexin-B1 (O43157) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P11684 · AlphaFold monomer V2.0 prediction for uteroglobin (P11684) · a predicted model of the same protein · chain B against A, TM-score 0.45
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
- Every structure of UniProt P11684
- Elsewhere: RCSB PDB 7VF3 · PDBe 7VF3 · UniProt O43157 · UniProt P11684
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.