Research workbench
Cryo-EM structure of the anti-feeding prophage (afp) baseplate in contracted state
Analyse Cryo-EM structure of the anti-feeding prophage (afp) baseplate in contracted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RGL
- Type
- protein
- Length
- 1,437 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFP2; AFP3; AFP4
- UniProt
- Q6HAD7, Q6HAD6, Q6HAD5
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 29% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | AFP2 | protein | 348 | 29% helix, 9% strand | Q6HAD7 |
| C | AFP3 | protein | 355 | 26% helix, 14% strand | Q6HAD6 |
| D | AFP4 | protein | 386 | 31% helix, 12% strand | Q6HAD5 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.82 | 0.83 | 102 | empty |
| 2 | 889 | 0.80 | 0.82 | 68 | empty |
| 3 | 159 | 0.79 | 0.95 | 34 | empty |
| 4 | 77 | 0.74 | 0.97 | 27 | empty |
| 5 | 322 | 0.71 | 0.84 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1658 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1233 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 823 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 3 hydrogen bonds · protein-protein
- B–A · 515 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6RGL · Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in contracted state · the same entry in another collection · chain B against B, 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 Q6HAD7
- Every structure of UniProt Q6HAD6
- Every structure of UniProt Q6HAD5
- Elsewhere: RCSB PDB 6RGL · PDBe 6RGL · UniProt Q6HAD7 · UniProt Q6HAD6 · UniProt Q6HAD5
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