MolNFT v1 · #27246 · protein
The structure and function of xenopus NO38-core, a histone binding chaperone in the nucleolus
1XE0 · Nucleophosmin: “The structure and function of xenopus NO38-core, a histone binding chaperone in the nucleolus”. X-ray diffraction, 10 pockets (best druggability 0.89). MolNFT v1 #27246 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1XE0
- Type
- protein
- Length
- 1,050 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleophosmin
- UniProt
- P07222
- Pockets
- 10 · best druggability 0.89
Structure
x-ray diffraction · 10 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleophosmin | protein | 108 | 0% helix, 64% strand | P07222 |
| B | Nucleophosmin | protein | 107 | 0% helix, 66% strand | P07222 |
| C | Nucleophosmin | protein | 101 | 0% helix, 65% strand | P07222 |
| D | Nucleophosmin | protein | 105 | 0% helix, 63% strand | P07222 |
| E | Nucleophosmin | protein | 104 | 0% helix, 66% strand | P07222 |
| F | Nucleophosmin | protein | 108 | 0% helix, 67% strand | P07222 |
| G | Nucleophosmin | protein | 104 | 0% helix, 63% strand | P07222 |
| H | Nucleophosmin | protein | 104 | 0% helix, 66% strand | P07222 |
| I | Nucleophosmin | protein | 105 | 0% helix, 66% strand | P07222 |
| J | Nucleophosmin | protein | 104 | 0% helix, 64% strand | P07222 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.89 | 0.90 | 150 | empty |
| 2 | 81 | 0.58 | 0.88 | 21 | empty |
| 3 | 52 | 0.53 | 0.88 | 18 | empty |
| 4 | 57 | 0.52 | 0.87 | 15 | empty |
| 5 | 136 | 0.49 | 0.78 | 33 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1055 Ų buried · 22 hydrogen bonds · protein-protein
- H–I · 1049 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1044 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1044 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1019 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1XE0 · The structure and function of Xenopus NO38-core, a histone binding chaperone in the… · the same entry in another collection · chain J against J, TM-score 1.00
- P07222 · AlphaFold monomer V2.0 prediction for nucleophosmin (P07222) · a predicted model of the same protein · chain I against A, TM-score 0.99
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 P07222
- Elsewhere: RCSB PDB 1XE0 · PDBe 1XE0 · UniProt P07222
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