Research workbench
Structure of vaccinia virus D8 protein bound to human Fab VV66
Analyse Structure of vaccinia virus D8 protein bound to human Fab VV66 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5USH
- Type
- protein
- Length
- 1,307 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imv membrane protein; Fab VV66 heavy chain; Fab VV66 light chain
- UniProt
- Q1M1K6
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imv membrane protein | protein | 223 | 11% helix, 38% strand | Q1M1K6 |
| D | Fab VV66 heavy chain | protein | 216 | 7% helix, 54% strand | — |
| E, L | Fab VV66 light chain | protein | 212 | 7% helix, 50% strand | — |
| H | Fab VV66 heavy chain | protein | 214 | 6% helix, 53% strand | — |
| X | Imv membrane protein | protein | 230 | 11% helix, 37% strand | Q1M1K6 |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.67 | 0.78 | 64 | empty |
| 2 | 504 | 0.67 | 0.78 | 52 | empty |
| 3 | 224 | 0.54 | 0.78 | 36 | empty |
| 4 | 184 | 0.54 | 0.79 | 29 | empty |
| 5 | 230 | 0.53 | 0.77 | 40 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1670 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1666 Ų buried · 13 hydrogen bonds · protein-protein
- H–X · 931 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 885 Ų buried · 22 hydrogen bonds · protein-protein
- E–L · 589 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5USH · Structure of vaccinia virus D8 protein bound to human Fab vv66 · 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 Q1M1K6
- Elsewhere: RCSB PDB 5USH · PDBe 5USH · UniProt Q1M1K6
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