MolNFT v1 · #139868 · protein
Crystal structure of the marburg virus nucleoprotein core domain chaperoned by a VP35 peptide
5XSQ: “Crystal structure of the marburg virus nucleoprotein core domain chaperoned by a VP35 peptide”. X-ray diffraction, 5 pockets (best druggability 0.79). MolNFT v1 #139868 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XSQ
- Type
- protein
- Length
- 1,013 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; Peptide from polymerase cofactor VP35
- UniProt
- Q6UY69, Q6UY68
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nucleoprotein | protein | 316 | 61% helix, 5% strand | Q6UY69 |
| B, D, F | Peptide from polymerase cofactor VP35 | protein | 23 | 57% helix, 0% strand | Q6UY68 |
| E | Nucleoprotein | protein | 312 | 62% helix, 5% strand | Q6UY69 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.79 | 0.81 | 113 | empty |
| 2 | 123 | 0.45 | 0.78 | 21 | empty |
| 3 | 67 | 0.33 | 0.76 | 13 | empty |
| 4 | 55 | 0.30 | 0.76 | 13 | empty |
| 5 | 73 | 0.30 | 0.73 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–C · 962 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 895 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 891 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 891 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 235 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XSQ · Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35… · 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 Q6UY69
- Every structure of UniProt Q6UY68
- Elsewhere: RCSB PDB 5XSQ · PDBe 5XSQ · UniProt Q6UY69 · UniProt Q6UY68
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