MolNFT v1 · #182596 · protein
Cryo-EM structure of pffnt-inhibitor complex
7MXY · Formate-nitrite transporter: “Cryo-EM structure of pffnt-inhibitor complex”. Electron microscopy, 1 ligand (HV6), 17 pockets (best druggability 0.87). MolNFT v1 #182596 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MXY
- Type
- protein
- Length
- 1,406 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate-nitrite transporter
- UniProt
- O77389
- Ligands
- HV6
- Pockets
- 17 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 77% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate-nitrite transporter | protein | 283 | 76% helix, 2% strand | O77389 |
| B | Formate-nitrite transporter | protein | 281 | 78% helix, 2% strand | O77389 |
| C | Formate-nitrite transporter | protein | 279 | 78% helix, 1% strand | O77389 |
| D | Formate-nitrite transporter | protein | 282 | 77% helix, 2% strand | O77389 |
| E | Formate-nitrite transporter | protein | 281 | 78% helix, 2% strand | O77389 |
Ligands and binding sites
- HV6 · (Z)-4,4,5,5,5-pentakis(fluoranyl)-1-(4-methoxy-2-oxidanyl-phenyl)-3-oxidanyl-pent-2-en-1-one · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.87 | 0.87 | 57 | empty |
| 2 | 619 | 0.77 | 0.82 | 55 | HV6 |
| 3 | 546 | 0.76 | 0.83 | 49 | HV6 |
| 4 | 463 | 0.76 | 0.84 | 53 | empty |
| 5 | 505 | 0.75 | 0.83 | 48 | HV6 |
Interfaces
10 interfaces between chains.
- A–C · 2051 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 2046 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2043 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2043 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 2018 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7MXY · Cryo-EM structure of PfFNT-inhibitor complex · 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 O77389
- Elsewhere: RCSB PDB 7MXY · PDBe 7MXY · UniProt O77389
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