MolNFT v1 · #170085 · protein
Crystal structure of murine norovirus P domain in complex with nanobody nb-5820
6XW5 · Capsid protein: “Crystal structure of murine norovirus P domain in complex with nanobody nb-5820”. X-ray diffraction, 15 pockets (best druggability 0.86). MolNFT v1 #170085 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6XW5
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody nb-5820
- UniProt
- Q80J94
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 305 | 6% helix, 39% strand | Q80J94 |
| B | Capsid protein | protein | 306 | 6% helix, 40% strand | Q80J94 |
| C | Nanobody nb-5820 | protein | 117 | 8% helix, 55% strand | — |
| D | Nanobody nb-5820 | protein | 120 | 10% helix, 54% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.86 | 0.91 | 65 | EDO |
| 2 | 103 | 0.63 | 0.89 | 29 | empty |
| 3 | 101 | 0.63 | 0.89 | 25 | empty |
| 4 | 161 | 0.56 | 0.81 | 24 | empty |
| 5 | 105 | 0.49 | 0.81 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1951 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 814 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 782 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6XW5 · Crystal structure of murine norovirus P domain in complex with Nanobody NB-5820 · 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 Q80J94
- Elsewhere: RCSB PDB 6XW5 · PDBe 6XW5 · UniProt Q80J94
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