MolNFT v1 · #95925 · protein
Pentameric sftsvn with suramin
4J4V · Nucleocapsid protein: “Pentameric sftsvn with suramin”. X-ray diffraction, 1 ligand (SVR), 11 pockets (best druggability 0.82). MolNFT v1 #95925 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4J4V
- Type
- protein
- Length
- 1,215 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid protein
- UniProt
- I6WJ72
- Ligands
- SVR
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid protein | protein | 244 | 69% helix, 1% strand | I6WJ72 |
| B | Nucleocapsid protein | protein | 240 | 67% helix, 1% strand | I6WJ72 |
| C | Nucleocapsid protein | protein | 245 | 65% helix, 1% strand | I6WJ72 |
| E | Nucleocapsid protein | protein | 240 | 68% helix, 1% strand | I6WJ72 |
| D | Nucleocapsid protein | protein | 246 | 67% helix, 1% strand | I6WJ72 |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · 5 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.82 | 0.83 | 127 | SVR |
| 2 | 288 | 0.73 | 0.86 | 48 | SVR |
| 3 | 291 | 0.73 | 0.86 | 50 | SVR |
| 4 | 208 | 0.71 | 0.87 | 52 | SVR |
| 5 | 163 | 0.59 | 0.82 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1690 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1676 Ų buried · 15 hydrogen bonds · protein-protein
- E–D · 1647 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1629 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1579 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4J4V · Pentameric SFTSVN with suramin · 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 I6WJ72
- Elsewhere: RCSB PDB 4J4V · PDBe 4J4V · UniProt I6WJ72
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