Research workbench
Cryo-EM structure of the anti-feeding prophage cap (afp tube terminating cap)
Analyse Cryo-EM structure of the anti-feeding prophage cap (afp tube terminating cap) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAP
- Type
- protein
- Length
- 1,279 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFP1; AFP2; AFP3; AFP16
- UniProt
- Q6HAD8, Q6HAD7, Q6HAD6, Q6HAC3
- Pockets
- 18 · best druggability 0.75
Structure
electron microscopy · 5 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | AFP1 | protein | 148 | 5% helix, 44% strand | Q6HAD8 |
| A | AFP1 | protein | 149 | 3% helix, 40% strand | Q6HAD8 |
| C | AFP2 | protein | 349 | 27% helix, 15% strand | Q6HAD7 |
| D | AFP3 | protein | 358 | 28% helix, 16% strand | Q6HAD6 |
| E | AFP16 | protein | 275 | 25% helix, 17% strand | Q6HAC3 |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.75 | 0.80 | 73 | empty |
| 2 | 873 | 0.75 | 0.79 | 68 | empty |
| 3 | 519 | 0.69 | 0.79 | 61 | empty |
| 4 | 441 | 0.65 | 0.78 | 51 | empty |
| 5 | 120 | 0.58 | 0.85 | 27 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1538 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1413 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 711 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 664 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 617 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6RAP · Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap) · 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 Q6HAD8
- Every structure of UniProt Q6HAD7
- Every structure of UniProt Q6HAD6
- Every structure of UniProt Q6HAC3
- Elsewhere: RCSB PDB 6RAP · PDBe 6RAP · UniProt Q6HAD8 · UniProt Q6HAD7 · UniProt Q6HAD6 · UniProt Q6HAC3
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