MolNFT v1 · #122940 · protein
Crystal structure of the L-ARGININE/AGMATINE antiporter adic in complex with agmatine at 2.6 angstroem resolution
5J4N: “Crystal structure of the L-ARGININE/AGMATINE antiporter adic in complex with agmatine at 2.6 angstroem…”. X-ray diffraction, 1 ligand (AG2), 12 pockets (best druggability 0.78). MolNFT v1 #122940 on GenesisL1: 3D structure, binding…
- PDB
- 5J4N
- 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
- AG2
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ARGININE/AGMATINE antiporter | protein | 437 | 78% helix, 0% strand | P60063 |
| B | ARGININE/AGMATINE antiporter | protein | 436 | 81% helix, 0% strand | P60063 |
Ligands and binding sites
- AG2 · Agmatine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.78 | 0.99 | 24 | empty |
| 2 | 643 | 0.72 | 0.79 | 60 | AG2 |
| 3 | 461 | 0.69 | 0.80 | 42 | AG2 |
| 4 | 207 | 0.53 | 0.77 | 21 | empty |
| 5 | 183 | 0.51 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2616 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5J4N · Crystal structure of the L-arginine/agmatine antiporter AdiC in complex with agmatine at… · 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 A 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 5J4N · PDBe 5J4N · UniProt P60063
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