Research workbench
Structure of vaccinia virus D8 protein bound to human Fab VV304
Analyse Structure of vaccinia virus D8 protein bound to human Fab VV304 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5USL
- Type
- protein
- Length
- 1,297 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imv membrane protein; Fab VV304 heavy chain; Fab VV304 light chain
- UniProt
- Q1M1K6
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Imv membrane protein | protein | 227 | 11% helix, 37% strand | Q1M1K6 |
| A | Imv membrane protein | protein | 226 | 12% helix, 38% strand | Q1M1K6 |
| H | Fab VV304 heavy chain | protein | 213 | 3% helix, 51% strand | — |
| L, C | Fab VV304 light chain | protein | 210 | 6% helix, 49% strand | — |
| B | Fab VV304 heavy chain | protein | 211 | 1% helix, 45% strand | — |
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 | 463 | 0.70 | 0.81 | 55 | empty |
| 2 | 319 | 0.68 | 0.82 | 37 | empty |
| 3 | 608 | 0.62 | 0.74 | 65 | empty |
| 4 | 560 | 0.61 | 0.74 | 52 | empty |
| 5 | 147 | 0.53 | 0.80 | 25 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1816 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1801 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 555 Ų buried · 6 hydrogen bonds · protein-protein
- X–H · 552 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5USL · Structure of vaccinia virus D8 protein bound to human Fab vv304 · the same entry in another collection · chain X against X, 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 5USL · PDBe 5USL · UniProt Q1M1K6
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