MolNFT v1 · #185841 · protein
Structure of magnesium-bound elenrmt in complex with two nanobodies at 4.1A
7QIC · Divalent metal cation transporter: “Structure of magnesium-bound elenrmt in complex with two nanobodies at 4.1A”. Electron microscopy, 1 ligand (MG), 8 pockets (best druggability 0.73). MolNFT v1 #185841 on GenesisL1: 3D structure…
- PDB
- 7QIC
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Divalent metal cation transporter; Nanobody 1; Nanobody 2
- UniProt
- A0A369N1S1
- Ligands
- MG
- Pockets
- 8 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Divalent metal cation transporter | protein | 401 | 78% helix, 0% strand | A0A369N1S1 |
| C | Nanobody 1 | protein | 117 | 0% helix, 33% strand | — |
| B | Nanobody 2 | protein | 121 | 2% helix, 29% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.73 | 0.81 | 51 | MG |
| 2 | 200 | 0.60 | 0.81 | 28 | empty |
| 3 | 203 | 0.50 | 0.76 | 37 | empty |
| 4 | 139 | 0.43 | 0.75 | 17 | empty |
| 5 | 138 | 0.38 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 665 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 201 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7QIC · Structure of magnesium-bound EleNRMT in complex with two nanobodies at 4.1A · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A369N1S1
- Elsewhere: RCSB PDB 7QIC · PDBe 7QIC · UniProt A0A369N1S1
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