Research workbench
Cryo-EM structure of vaccinia virus scaffolding protein D13 trimer sextet
Analyse Cryo-EM structure of vaccinia virus scaffolding protein D13 trimer sextet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VFH
- Type
- protein
- Length
- 9,486 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, L, J, K, N, O, M, Q, R, P | 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 | 919 | 0.85 | 0.86 | 97 | empty |
| 2 | 1010 | 0.84 | 0.85 | 100 | empty |
| 3 | 1068 | 0.84 | 0.85 | 95 | empty |
| 4 | 1141 | 0.84 | 0.85 | 111 | empty |
| 5 | 1135 | 0.84 | 0.85 | 100 | empty |
Interfaces
36 interfaces between chains.
- N–O · 2157 Ų buried · 16 hydrogen bonds · protein-protein
- G–I · 2151 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2146 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 2143 Ų buried · 19 hydrogen bonds · protein-protein
- R–P · 2143 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7VFH · Cryo-EM structure of Vaccinia virus scaffolding protein D13 trimer sextet · 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 P68440
- Elsewhere: RCSB PDB 7VFH · PDBe 7VFH · UniProt P68440
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