Research workbench
Cryo-EM structure of the anti-feeding prophage (afp) baseplate in extended state, 3-fold symmetrised
Analyse Cryo-EM structure of the anti-feeding prophage (afp) baseplate in extended… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RBK
- Type
- protein
- Length
- 951 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFP7; AFP8
- UniProt
- Q6HAD2, Q6HAD1
- Pockets
- 10 · best druggability 0.71
Structure
electron microscopy · 3 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AFP7 | protein | 223 | 15% helix, 26% strand | Q6HAD2 |
| B | AFP7 | protein | 224 | 15% helix, 27% strand | Q6HAD2 |
| C | AFP8 | protein | 504 | 7% helix, 26% strand | Q6HAD1 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.71 | 0.79 | 58 | empty |
| 2 | 360 | 0.61 | 0.78 | 28 | empty |
| 3 | 171 | 0.53 | 0.80 | 25 | empty |
| 4 | 121 | 0.47 | 0.79 | 22 | empty |
| 5 | 127 | 0.47 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1770 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 803 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6RBK · Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold… · the same entry in another collection · chain A against A, 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 Q6HAD2
- Every structure of UniProt Q6HAD1
- Elsewhere: RCSB PDB 6RBK · PDBe 6RBK · UniProt Q6HAD2 · UniProt Q6HAD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.