MolNFT v1 · #15995 · protein
The crystal structure of drosophila nlp-core provides insight into pentamer formation and histone binding
1NLQ · Nucleoplasmin-like protein: “The crystal structure of drosophila nlp-core provides insight into pentamer formation and histone binding”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.82). MolNFT v1 #15995 on…
- PDB
- 1NLQ
- Type
- protein
- Length
- 490 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoplasmin-like protein
- UniProt
- Q27415
- Ligands
- MG
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoplasmin-like protein | protein | 105 | 3% helix, 59% strand | Q27415 |
| B | Nucleoplasmin-like protein | protein | 97 | 3% helix, 63% strand | Q27415 |
| C | Nucleoplasmin-like protein | protein | 96 | 3% helix, 63% strand | Q27415 |
| D | Nucleoplasmin-like protein | protein | 94 | 0% helix, 62% strand | Q27415 |
| E | Nucleoplasmin-like protein | protein | 98 | 3% helix, 62% strand | Q27415 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.82 | 0.84 | 55 | empty |
Interfaces
5 interfaces between chains.
- C–E · 913 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 910 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 898 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 855 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1NLQ · The crystal structure of Drosophila NLP-core provides insight into pentamer formation and… · the same entry in another collection · chain E against E, TM-score 1.00
- Q27415 · AlphaFold monomer V2.0 prediction for nucleoplasmin-like protein (Q27415) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q27415
- Elsewhere: RCSB PDB 1NLQ · PDBe 1NLQ · UniProt Q27415
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