MolNFT v1 · #114265 · protein
Crystal structure of nucleoprotein-nucleozin complex
5B7B: “Crystal structure of nucleoprotein-nucleozin complex”. X-ray diffraction, 1 ligand (NUZ), 20 pockets (best druggability 0.82). MolNFT v1 #114265 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B7B
- Type
- protein
- Length
- 2,533 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- Q1K9H2
- Ligands
- NUZ
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 422 | 46% helix, 10% strand | Q1K9H2 |
| B | Nucleoprotein | protein | 423 | 47% helix, 9% strand | Q1K9H2 |
| C, F | Nucleoprotein | protein | 424 | 46% helix, 9% strand | Q1K9H2 |
| D | Nucleoprotein | protein | 419 | 48% helix, 10% strand | Q1K9H2 |
| E | Nucleoprotein | protein | 421 | 48% helix, 9% strand | Q1K9H2 |
Ligands and binding sites
- NUZ · [4-(2-chloro-4-nitrophenyl)piperazin-1-yl](5-methyl-3-phenyl-1,2-oxazol-4-yl)methanone · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.82 | 0.83 | 95 | empty |
| 2 | 731 | 0.78 | 0.82 | 75 | empty |
| 3 | 1009 | 0.76 | 0.79 | 101 | NUZ |
| 4 | 407 | 0.70 | 0.82 | 49 | NUZ |
| 5 | 162 | 0.69 | 0.88 | 23 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2385 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2296 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 2049 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2024 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 2020 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5B7B · Crystal structure of Nucleoprotein-nucleozin complex · the same entry in another collection · chain F against F, 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 Q1K9H2
- Elsewhere: RCSB PDB 5B7B · PDBe 5B7B · UniProt Q1K9H2
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