MolNFT v1 · #176553 · protein
A nicotine mate transporter, nicotiana tabacum MATE2 (NTMATE2)
7DQK · Protein detoxification: “A nicotine mate transporter, nicotiana tabacum MATE2 (NTMATE2)”. X-ray diffraction, 2 ligands (PO4, CL), 12 pockets (best druggability 0.84). MolNFT v1 #176553 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DQK
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein detoxification
- UniProt
- A3KDM5
- Ligands
- PO4, CL
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein detoxification | protein | 476 | 85% helix, 0% strand | A3KDM5 |
| B | Protein detoxification | protein | 479 | 84% helix, 0% strand | A3KDM5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
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 | 1043 | 0.84 | 0.85 | 87 | PO4 |
| 2 | 1012 | 0.82 | 0.83 | 71 | PO4 |
| 3 | 286 | 0.52 | 0.74 | 29 | empty |
| 4 | 210 | 0.52 | 0.76 | 22 | empty |
| 5 | 92 | 0.48 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 367 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7DQK · A nicotine MATE transporter, Nicotiana tabacum MATE2 (NtMATE2) · 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 A3KDM5
- Elsewhere: RCSB PDB 7DQK · PDBe 7DQK · UniProt A3KDM5
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