MolNFT v2 · #228615 · protein
Endophilin B1 dimers bound to nanodiscs
9G2R · Endophilin-B1: “Endophilin B1 dimers bound to nanodiscs”. Electron microscopy at 3.88, 20 pockets (best druggability 0.80). MolNFT v2 #228615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 9G2R
- Type
- protein
- Length
- 2,824 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.88
- Source
- Homo sapiens
- Molecule
- Endophilin-B1
- UniProt
- Q9Y371
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 3.88 · 3 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endophilin-B1 | protein | 228 | 89% helix, 0% strand | Q9Y371 |
| E, G, I, K | Endophilin-B1 | protein | 242 | 86% helix, 0% strand | Q9Y371 |
| F, H, J, L | Endophilin-B1 | protein | 236 | 87% helix, 0% strand | Q9Y371 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.80 | 0.88 | 42 | empty |
| 2 | 416 | 0.79 | 0.88 | 40 | empty |
| 3 | 991 | 0.79 | 0.80 | 68 | empty |
| 4 | 952 | 0.79 | 0.80 | 70 | empty |
| 5 | 977 | 0.78 | 0.80 | 74 | empty |
Interfaces
16 interfaces between chains.
- G–H · 2380 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 2374 Ų buried · 2 hydrogen bonds · protein-protein
- K–L · 2364 Ų buried · 2 hydrogen bonds · protein-protein
- I–J · 2364 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 2292 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- Q9Y371 · AlphaFold monomer V2.0 prediction for endophilin-B1 (Q9Y371) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 Q9Y371
- Elsewhere: RCSB PDB 9G2R · PDBe 9G2R · UniProt Q9Y371
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