Research workbench
Crystal structure of the cytosolic domain of human CNNM2 in complex with AMP-pnp and MG2+
Analyse Crystal structure of the cytosolic domain of human CNNM2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7E
- Type
- protein
- Length
- 1,226 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal transporter CNNM2,METAL transporter CNNM2
- UniProt
- Q9H8M5
- Ligands
- ANP, MG
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metal transporter CNNM2,METAL transporter CNNM2 | protein | 305 | 32% helix, 23% strand | Q9H8M5 |
| B | Metal transporter CNNM2,METAL transporter CNNM2 | protein | 300 | 33% helix, 23% strand | Q9H8M5 |
| C | Metal transporter CNNM2,METAL transporter CNNM2 | protein | 302 | 31% helix, 21% strand | Q9H8M5 |
| D | Metal transporter CNNM2,METAL transporter CNNM2 | protein | 319 | 29% helix, 22% strand | Q9H8M5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.87 | 0.88 | 89 | ANP, MG |
| 2 | 1136 | 0.83 | 0.84 | 101 | ANP, MG |
| 3 | 951 | 0.71 | 0.75 | 96 | empty |
| 4 | 72 | 0.53 | 0.86 | 20 | empty |
| 5 | 96 | 0.47 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2001 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1887 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 700 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 601 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 597 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6N7E · Crystal structure of the cytosolic domain of human CNNM2 in complex with AMP-PNP and Mg2+ · the same entry in another collection · chain D against D, TM-score 1.00
- Q9H8M5 · AlphaFold monomer V2.0 prediction for metal transporter CNNM2 (Q9H8M5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9H8M5
- Elsewhere: RCSB PDB 6N7E · PDBe 6N7E · UniProt Q9H8M5
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