Research workbench
X-ray structure of a MN2+ soak of elenrmt in complex with two nanobodies at 4.6A
Analyse X-ray structure of a MN2+ soak of elenrmt in complex with two nanobodies at 4.6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QJJ
- Type
- protein
- Length
- 1,272 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Divalent metal cation transporter; Elen-NB1-NB2
- UniProt
- A0A369N1S1
- Ligands
- MN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Divalent metal cation transporter | protein | 398 | 77% helix, 0% strand | A0A369N1S1 |
| C, F | Elen-NB1-NB2 | protein | 117 | 0% helix, 38% strand | — |
| B, G | Elen-NB1-NB2 | protein | 121 | 7% helix, 30% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, E
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 | 562 | 0.74 | 0.81 | 47 | MN |
| 2 | 585 | 0.74 | 0.81 | 51 | MN |
| 3 | 229 | 0.66 | 0.84 | 31 | empty |
| 4 | 206 | 0.66 | 0.84 | 30 | empty |
| 5 | 259 | 0.50 | 0.74 | 36 | empty |
Interfaces
6 interfaces between chains.
- E–F · 687 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 677 Ų buried · 14 hydrogen bonds · protein-protein
- E–G · 591 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 591 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 194 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7QJJ · X-Ray Structure of a Mn2+ soak of EleNRMT in complex with two Nanobodies at 4.6A · 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 7QJJ · PDBe 7QJJ · UniProt A0A369N1S1
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