MolNFT v1 · #175857 · protein
Structure of mrp complex from dietzia sp. DQ12-45-1B
7D3U · Monovalent NA+/H+ antiporter subunit D: “Structure of mrp complex from dietzia sp. DQ12-45-1B”. Electron microscopy, 20 pockets (best druggability 0.74). MolNFT v1 #175857 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7D3U
- Type
- protein
- Length
- 1,873 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monovalent NA+/H+ antiporter subunit D; Monovalent NA+/H+ antiporter subunit a…
- UniProt
- A0A221C8X0, A0A221C8X2, A0A221C8X5, A0A221C8X7, A0A221C8Y4, A0A221C8X1
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 6 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Monovalent NA+/H+ antiporter subunit D | protein | 534 | 66% helix, 3% strand | A0A221C8X0 |
| A | Monovalent NA+/H+ antiporter subunit a | protein | 904 | 68% helix, 2% strand | A0A221C8X2 |
| C | Monovalent NA+/H+ antiporter subunit C | protein | 129 | 50% helix, 2% strand | A0A221C8X5 |
| F | Monovalent NA+/H+ antiporter subunit F | protein | 85 | 73% helix, 0% strand | A0A221C8X7 |
| G | Monovalent NA+/H+ antiporter subunit G | protein | 111 | 70% helix, 2% strand | A0A221C8Y4 |
| E | Cation antiporter | protein | 110 | 48% helix, 17% strand | A0A221C8X1 |
Ligands and binding sites
- LMT · Dodecyl-beta-D-maltoside · additive · 28 copies · chains D, A, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.74 | 0.85 | 28 | LMT |
| 2 | 159 | 0.73 | 0.90 | 30 | LMT |
| 3 | 172 | 0.72 | 0.90 | 43 | empty |
| 4 | 50 | 0.68 | 0.97 | 21 | empty |
| 5 | 693 | 0.67 | 0.75 | 69 | empty |
Interfaces
9 interfaces between chains.
- D–A · 4811 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 4648 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 2400 Ų buried · 7 hydrogen bonds · protein-protein
- D–C · 2116 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1935 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7D3U · Structure of Mrp complex from Dietzia sp. DQ12-45-1b · the same entry in another collection · chain D against D, 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 A0A221C8X0
- Every structure of UniProt A0A221C8X2
- Every structure of UniProt A0A221C8X5
- Every structure of UniProt A0A221C8X7
- Every structure of UniProt A0A221C8Y4
- Every structure of UniProt A0A221C8X1
- Elsewhere: RCSB PDB 7D3U · PDBe 7D3U · UniProt A0A221C8X0 · UniProt A0A221C8X2 · UniProt A0A221C8X5 · UniProt A0A221C8X7 · UniProt A0A221C8Y4 · UniProt A0A221C8X1
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