MolNFT v1 · #159163 · protein
Cryo-EM structure of yentca in its prepore state
6OGD · Toxin subunit YENA1: “Cryo-EM structure of yentca in its prepore state”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #159163 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OGD
- Type
- protein
- Length
- 11,820 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin subunit YENA1; Toxin subunit YENA2; Chitinase 2
- EC
- 3.2.1.14
- UniProt
- B6A877, B6A878, B6A879
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M | Toxin subunit YENA1 | protein | 748 | 59% helix, 0% strand | B6A877 |
| B, E, H, K, N | Toxin subunit YENA2 | protein | 1078 | 47% helix, 9% strand | B6A878 |
| C, F, I, L, O | Chitinase 2 (EC 3.2.1.14) | protein | 538 | 29% helix, 14% strand | B6A879 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.88 | 0.90 | 126 | empty |
| 2 | 764 | 0.88 | 0.91 | 106 | empty |
| 3 | 1178 | 0.87 | 0.87 | 145 | empty |
| 4 | 644 | 0.86 | 0.90 | 94 | empty |
| 5 | 979 | 0.84 | 0.85 | 96 | empty |
Interfaces
35 interfaces between chains.
- B–E · 6842 Ų buried · 66 hydrogen bonds · protein-protein
- K–N · 6834 Ų buried · 64 hydrogen bonds · protein-protein
- E–H · 6833 Ų buried · 64 hydrogen bonds · protein-protein
- H–K · 6797 Ų buried · 64 hydrogen bonds · protein-protein
- B–N · 6790 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 6OGD · Cryo-EM structure of YenTcA in its prepore state · the same entry in another collection · chain H against H, TM-score 1.00
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 B6A877
- Every structure of UniProt B6A878
- Every structure of UniProt B6A879
- Elsewhere: RCSB PDB 6OGD · PDBe 6OGD · UniProt B6A877 · UniProt B6A878 · UniProt B6A879
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