Research workbench
Fitting of GP8 structure into the cryoem reconstruction of the bacteriophage T4 baseplate
Analyse Fitting of GP8 structure into the cryoem reconstruction of the bacteriophage T4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PDM
- Type
- protein
- Length
- 3,936 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate structural protein GP8
- UniProt
- P19062
- Pockets
- 3 · best druggability 0.31
Structure
electron microscopy · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Baseplate structural protein GP8 | protein | 328 | 0% helix, 0% strand | P19062 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.31 | 0.73 | 23 | empty |
| 2 | 66 | 0.29 | 0.72 | 21 | empty |
| 3 | 52 | 0.28 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- I–J · 387 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 386 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 384 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 382 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PDM · Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate · 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 P19062
- Elsewhere: RCSB PDB 1PDM · PDBe 1PDM · UniProt P19062
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