Research workbench
Cryo-EM structure of the anti-feeding prophage (afp) baseplate, 6-fold symmetrised
Analyse Cryo-EM structure of the anti-feeding prophage (afp) baseplate, 6-fold… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAO
- Type
- protein
- Length
- 2,880 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFP1; AFP2; AFP3; AFP5; AFP9; AFP4; AFP7; AFP11; AFP12
- UniProt
- Q6HAD8, Q6HAD7, Q6HAD6, Q6HAD4, Q6HAD0, Q6HAD5, Q6HAD2, Q6HAC8, Q6HAC7
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 9 distinct chains · 26% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AFP1 | protein | 148 | 5% helix, 44% strand | Q6HAD8 |
| C | AFP2 | protein | 351 | 28% helix, 16% strand | Q6HAD7 |
| D | AFP3 | protein | 358 | 29% helix, 16% strand | Q6HAD6 |
| F | AFP5 | protein | 149 | 5% helix, 39% strand | Q6HAD4 |
| H | AFP9 | protein | 125 | 35% helix, 18% strand | Q6HAD0 |
| E | AFP4 | protein | 386 | 33% helix, 17% strand | Q6HAD5 |
| G | AFP7 | protein | 224 | 15% helix, 25% strand | Q6HAD2 |
| I | AFP11 | protein | 443 | 27% helix, 16% strand | Q6HAC8 |
| J | AFP12 | protein | 548 | 32% helix, 6% strand | Q6HAC7 |
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 | 104 | 0.77 | 0.97 | 20 | empty |
| 2 | 1150 | 0.75 | 0.78 | 109 | empty |
| 3 | 876 | 0.74 | 0.78 | 76 | empty |
| 4 | 1096 | 0.72 | 0.75 | 93 | empty |
| 5 | 575 | 0.71 | 0.80 | 62 | empty |
Interfaces
18 interfaces between chains.
- I–J · 3958 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 1743 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1699 Ų buried · 26 hydrogen bonds · protein-protein
- H–E · 1532 Ų buried · 22 hydrogen bonds · protein-protein
- H–J · 1247 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RAO · Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold symmetrised · the same entry in another collection · chain J against J, 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 Q6HAD4
- Every structure of UniProt Q6HAD0
- Every structure of UniProt Q6HAD5
- Every structure of UniProt Q6HAD2
- Every structure of UniProt Q6HAC8
- Every structure of UniProt Q6HAC7
- Elsewhere: RCSB PDB 6RAO · PDBe 6RAO · UniProt Q6HAD8 · UniProt Q6HAD7 · UniProt Q6HAD6 · UniProt Q6HAD4 · UniProt Q6HAD0 · UniProt Q6HAD5 · UniProt Q6HAD2 · UniProt Q6HAC8 · UniProt Q6HAC7
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