Research workbench
GII.10 vietnam 026 protruding domain in complex with nanobody nano-32
Analyse GII.10 vietnam 026 protruding domain in complex with nanobody nano-32 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O03
- Type
- protein
- Length
- 887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody (vhh) nano-32
- UniProt
- Q5F4T5
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 310 | 7% helix, 35% strand | Q5F4T5 |
| B | Capsid protein | protein | 312 | 7% helix, 36% strand | Q5F4T5 |
| C | Nanobody (vhh) nano-32 | protein | 132 | 7% helix, 41% strand | — |
| D | Nanobody (vhh) nano-32 | protein | 133 | 7% helix, 43% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.86 | 0.90 | 108 | EDO |
| 2 | 454 | 0.73 | 0.83 | 51 | EDO |
| 3 | 379 | 0.68 | 0.81 | 54 | EDO |
| 4 | 143 | 0.66 | 0.88 | 25 | EDO |
| 5 | 77 | 0.49 | 0.83 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1850 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 693 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5O03 · GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-32 · 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 Q5F4T5
- Elsewhere: RCSB PDB 5O03 · PDBe 5O03 · UniProt Q5F4T5
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