Research workbench
Structure of T7 DNA ejectosome periplasmic tunnel
Analyse Structure of T7 DNA ejectosome periplasmic tunnel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5C
- Type
- protein
- Length
- 5,268 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 0.81
Structure
electron microscopy · 2 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A, C, E, I, K | Internal virion protein GP15 | protein | 650 | 70% helix, 5% strand | P03725 |
| G, B, D, F, J, L | Peptidoglycan transglycosylase GP16 (EC 4.2.2.-) | protein | 228 | 43% 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 | 1061 | 0.81 | 0.83 | 127 | empty |
| 2 | 1026 | 0.78 | 0.80 | 90 | empty |
| 3 | 1018 | 0.78 | 0.80 | 102 | empty |
| 4 | 198 | 0.75 | 0.90 | 28 | empty |
| 5 | 536 | 0.75 | 0.83 | 71 | empty |
Interfaces
24 interfaces between chains.
- I–K · 4644 Ų buried · 63 hydrogen bonds · protein-protein
- H–A · 4641 Ų buried · 63 hydrogen bonds · protein-protein
- E–I · 4640 Ų buried · 61 hydrogen bonds · protein-protein
- C–E · 4639 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 4637 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 7K5C · Structure of T7 DNA ejectosome periplasmic tunnel · the same entry in another collection · chain H against H, 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 7K5C · PDBe 7K5C · UniProt P03725 · UniProt P03726
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