MolNFT v1 · #117389 · protein
PLEXINB2 cytoplasmic REGION/PDZ-rhogef PDZ domain complex
5E6P · Plexin-B2: “PLEXINB2 cytoplasmic REGION/PDZ-rhogef PDZ domain complex”. X-ray diffraction, 7 pockets (best druggability 0.63). MolNFT v1 #117389 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E6P
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-B2; Rho guanine nucleotide exchange factor 11
- UniProt
- B2RXS4, O15085
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-B2 | protein | 504 | 57% helix, 9% strand | B2RXS4 |
| B | Rho guanine nucleotide exchange factor 11 | protein | 75 | 12% helix, 39% strand | O15085 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.63 | 0.81 | 39 | empty |
| 2 | 108 | 0.45 | 0.78 | 14 | empty |
| 3 | 167 | 0.45 | 0.75 | 38 | empty |
| 4 | 96 | 0.43 | 0.78 | 21 | empty |
| 5 | 64 | 0.36 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 795 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5E6P · PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex · the same entry in another collection · chain A against A, TM-score 1.00
- B2RXS4 · AlphaFold monomer V2.0 prediction for plexin-B2 (B2RXS4) · a predicted model of the same protein · chain A against A, TM-score 0.96
- O15085 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 11 (O15085) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 B2RXS4
- Every structure of UniProt O15085
- Elsewhere: RCSB PDB 5E6P · PDBe 5E6P · UniProt B2RXS4 · UniProt O15085
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