MolNFT v1 · #183941 · protein
The L-ARGININE/AGMATINE antiporter from E. COLI at 1.7 a resolution
7O82: “The L-ARGININE/AGMATINE antiporter from E. COLI at 1.7 a resolution”. X-ray diffraction, 2 ligands (BNG, D10), 13 pockets (best druggability 0.76). MolNFT v1 #183941 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7O82
- Type
- protein
- Length
- 873 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARGININE/AGMATINE antiporter
- UniProt
- P60063
- Ligands
- BNG, D10
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ARGININE/AGMATINE antiporter | protein | 437 | 81% helix, 0% strand | P60063 |
| B | ARGININE/AGMATINE antiporter | protein | 436 | 80% helix, 0% strand | P60063 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 3 copies · chains A, B
- D10 · Decane · ligand · 2 copies · chains A, B
- HEX · Hexane · additive · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- OCT · N-octane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.76 | 0.99 | 22 | empty |
| 2 | 436 | 0.70 | 0.81 | 36 | empty |
| 3 | 473 | 0.70 | 0.80 | 38 | empty |
| 4 | 177 | 0.53 | 0.78 | 21 | empty |
| 5 | 153 | 0.48 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2661 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7O82 · The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P60063 · AlphaFold monomer V2.0 prediction for ARGININE/AGMATINE antiporter (P60063) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P60063
- Elsewhere: RCSB PDB 7O82 · PDBe 7O82 · UniProt P60063
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