Research workbench
Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - final EM refinement
Analyse Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - final… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YEG
- Type
- protein
- Length
- 2,064 residues
- Chains
- 12
- Method
- electron microscopy; solid-state nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail tube protein GP17.1*
- UniProt
- O48449
- Pockets
- 20 · best druggability 0.70
Structure
electron microscopy; solid-state nmr · 1 distinct chain · 7% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Tail tube protein GP17.1* | protein | 172 | 7% helix, 30% strand | O48449 |
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 | 714 | 0.70 | 0.77 | 79 | empty |
| 2 | 678 | 0.70 | 0.77 | 70 | empty |
| 3 | 199 | 0.68 | 0.86 | 25 | empty |
| 4 | 206 | 0.67 | 0.86 | 31 | empty |
| 5 | 208 | 0.67 | 0.86 | 29 | empty |
Interfaces
36 interfaces between chains.
- G–H · 1457 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 1448 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 1440 Ų buried · 24 hydrogen bonds · protein-protein
- J–K · 1440 Ų buried · 26 hydrogen bonds · protein-protein
- G–L · 1439 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6YEG · Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM… · 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 O48449
- Elsewhere: RCSB PDB 6YEG · PDBe 6YEG · UniProt O48449
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