MolNFT v1 · #50395 · protein
Crystal structure of nudc domain-containing protein 2 (13542905) from mus musculus at 1.95 a resolution
2RH0: “Crystal structure of nudc domain-containing protein 2 (13542905) from mus musculus at 1.95 a resolution”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #50395 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2RH0
- Type
- protein
- Length
- 528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudc domain-containing protein 2
- UniProt
- Q9CQ48
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudc domain-containing protein 2 | protein | 133 | 21% helix, 40% strand | Q9CQ48 |
| B, D | Nudc domain-containing protein 2 | protein | 132 | 19% helix, 41% strand | Q9CQ48 |
| C | Nudc domain-containing protein 2 | protein | 131 | 19% helix, 42% strand | Q9CQ48 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.65 | 0.79 | 40 | empty |
| 2 | 297 | 0.63 | 0.80 | 32 | EDO |
| 3 | 91 | 0.62 | 0.89 | 21 | empty |
| 4 | 94 | 0.62 | 0.88 | 21 | empty |
| 5 | 86 | 0.46 | 0.80 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5354 Ų buried · 87 hydrogen bonds · protein-protein
- C–D · 5287 Ų buried · 86 hydrogen bonds · protein-protein
- B–C · 297 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 180 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 175 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2RH0 · Crystal structure of NudC domain-containing protein 2 (13542905) from Mus musculus at… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CQ48 · AlphaFold monomer V2.0 prediction for nudc domain-containing protein 2 (Q9CQ48) · a predicted model of the same protein · chain C against A, TM-score 0.58
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 Q9CQ48
- Elsewhere: RCSB PDB 2RH0 · PDBe 2RH0 · UniProt Q9CQ48
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