MolNFT v2 · #216195 · protein
Homotypic interacting B1 fab bound to Chondroitin Sulfate A
8P2E · B1 fab light: “Homotypic interacting B1 fab bound to Chondroitin Sulfate A”. Electron microscopy at 3.2, 20 pockets (best druggability 0.78). MolNFT v2 #216195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8P2E
- Type
- protein
- Length
- 1,691 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens
- Molecule
- B1 fab light; B1 fab heavy
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 3.2 · 6 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B1 fab light | protein | 210 | 7% helix, 54% strand | — |
| B, D, F | B1 fab heavy | protein | 208 | 7% helix, 51% strand | — |
| C | B1 fab light | protein | 218 | 8% helix, 51% strand | — |
| E | B1 fab light | protein | 215 | 7% helix, 54% strand | — |
| G | B1 fab light | protein | 215 | 7% helix, 53% strand | — |
| H | B1 fab heavy | protein | 209 | 7% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.78 | 0.81 | 103 | empty |
| 2 | 903 | 0.71 | 0.76 | 103 | empty |
| 3 | 667 | 0.67 | 0.76 | 72 | empty |
| 4 | 248 | 0.60 | 0.80 | 39 | empty |
| 5 | 170 | 0.54 | 0.80 | 27 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1896 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1828 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1769 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1680 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 654 Ų buried · 12 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8P2E · PDBe 8P2E
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