Research workbench
Fitting of the GP6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate
Analyse Fitting of the GP6 crystal structure into 3D cryo-EM reconstruction of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H3W
- Type
- protein
- Length
- 3,900 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate structural protein GP6
- UniProt
- P19060
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Baseplate structural protein GP6 | protein | 326 | 14% helix, 30% strand | P19060 |
| B, D, F, H, J, L | Baseplate structural protein GP6 | protein | 324 | 19% helix, 32% strand | P19060 |
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 | 944 | 0.77 | 0.80 | 96 | empty |
| 2 | 1100 | 0.75 | 0.78 | 109 | empty |
| 3 | 587 | 0.73 | 0.80 | 70 | empty |
| 4 | 542 | 0.72 | 0.81 | 65 | empty |
| 5 | 756 | 0.71 | 0.77 | 77 | empty |
Interfaces
18 interfaces between chains.
- K–L · 1119 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1119 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1115 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1114 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1112 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3H3W · Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4… · 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 P19060
- Elsewhere: RCSB PDB 3H3W · PDBe 3H3W · UniProt P19060
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