Research workbench
Crystal structure of 2012 nsw GII.4 P domain in complex with nano-85
Analyse Crystal structure of 2012 nsw GII.4 P domain in complex with nano-85 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X7D
- Type
- protein
- Length
- 840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; Nano-85 nanobody
- UniProt
- K4LM89
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VP1 | protein | 307 | 5% helix, 35% strand | K4LM89 |
| C | Nano-85 nanobody | protein | 105 | 3% helix, 52% strand | — |
| D | Nano-85 nanobody | protein | 121 | 5% helix, 55% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.75 | 0.96 | 20 | EDO |
| 2 | 60 | 0.72 | 0.98 | 20 | empty |
| 3 | 401 | 0.67 | 0.80 | 56 | empty |
| 4 | 282 | 0.62 | 0.80 | 34 | empty |
| 5 | 153 | 0.54 | 0.81 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1724 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 772 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 760 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4X7D · Crystal structure of 2012 NSW GII.4 P domain in complex with Nano-85 · 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 K4LM89
- Elsewhere: RCSB PDB 4X7D · PDBe 4X7D · UniProt K4LM89
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