Research workbench
Cryo-EM structure of vaccinia virus scaffolding protein D13 trimer doublet
Analyse Cryo-EM structure of vaccinia virus scaffolding protein D13 trimer doublet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VFG
- Type
- protein
- Length
- 3,162 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, D, C, A, B | Scaffold protein D13 | protein | 527 | 17% helix, 41% strand | P68440 |
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 | 1184 | 0.84 | 0.84 | 112 | empty |
| 2 | 962 | 0.83 | 0.84 | 96 | empty |
| 3 | 1105 | 0.82 | 0.83 | 123 | empty |
| 4 | 709 | 0.81 | 0.85 | 60 | empty |
| 5 | 615 | 0.80 | 0.85 | 64 | empty |
Interfaces
9 interfaces between chains.
- C–A · 2125 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2121 Ų buried · 20 hydrogen bonds · protein-protein
- E–D · 2105 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 2094 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2049 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7VFG · Cryo-EM structure of Vaccinia virus scaffolding protein D13 trimer doublet · the same entry in another collection · chain E against E, 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 P68440
- Elsewhere: RCSB PDB 7VFG · PDBe 7VFG · UniProt P68440
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