Research workbench
Cryo-EM structure of T7 bacteriophage DNA translocation GP15-GP16 core complex intermediate assembly
Analyse Cryo-EM structure of T7 bacteriophage DNA translocation GP15-GP16 core complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YT5
- Type
- protein
- Length
- 5,040 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Internal virion protein GP15; Peptidoglycan transglycosylase GP16
- EC
- 4.2.2.-
- UniProt
- P03725, P03726
- Pockets
- 20 · best druggability 0.70
Structure
electron microscopy · 2 distinct chains · 59% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Internal virion protein GP15 | protein | 642 | 63% helix, 3% strand | P03725 |
| G, H, I, J, K, L | Peptidoglycan transglycosylase GP16 (EC 4.2.2.-) | protein | 198 | 44% helix, 0% strand | P03726 |
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 | 133 | 0.70 | 0.91 | 27 | empty |
| 2 | 413 | 0.68 | 0.81 | 59 | empty |
| 3 | 446 | 0.68 | 0.80 | 58 | empty |
| 4 | 118 | 0.67 | 0.90 | 27 | empty |
| 5 | 131 | 0.67 | 0.89 | 28 | empty |
Interfaces
24 interfaces between chains.
- B–C · 4977 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 4970 Ų buried · 68 hydrogen bonds · protein-protein
- D–E · 4969 Ų buried · 68 hydrogen bonds · protein-protein
- A–F · 4969 Ų buried · 68 hydrogen bonds · protein-protein
- E–F · 4961 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 6YT5 · Cryo-EM structure of T7 bacteriophage DNA translocation gp15-gp16 core complex… · 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 P03725
- Every structure of UniProt P03726
- Elsewhere: RCSB PDB 6YT5 · PDBe 6YT5 · UniProt P03725 · UniProt P03726
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