MolNFT v1 · #54373 · protein
Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor
2XMR · Protein NDRG2: “Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.68). MolNFT v1 #54373 on GenesisL1: 3D structure…
- PDB
- 2XMR
- Type
- protein
- Length
- 843 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein NDRG2
- UniProt
- Q9UN36
- Ligands
- CA
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein NDRG2 | protein | 281 | 42% helix, 18% strand | Q9UN36 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 611 | 0.68 | 0.77 | 57 | empty |
| 2 | 766 | 0.68 | 0.76 | 57 | empty |
| 3 | 235 | 0.64 | 0.83 | 30 | empty |
| 4 | 202 | 0.51 | 0.77 | 22 | empty |
| 5 | 178 | 0.48 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 488 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 441 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 387 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XMR · Crystal structure of human NDRG2 protein provides insight into its role as a tumor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UN36 · AlphaFold monomer V2.0 prediction for protein NDRG2 (Q9UN36) · a predicted model of the same protein · chain A 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 Q9UN36
- Elsewhere: RCSB PDB 2XMR · PDBe 2XMR · UniProt Q9UN36
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