MolNFT v1 · #72582 · protein
X-ray crystal structure of an arginine agmatine antiporter (adic) in complex with a Fab fragment
3NCY: “X-ray crystal structure of an arginine agmatine antiporter (adic) in complex with a Fab fragment”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #72582 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3NCY
- Type
- protein
- Length
- 2,540 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adic; Fab heavy chain; Fab light chain
- UniProt
- P60066
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adic | protein | 422 | 63% helix, 0% strand | P60066 |
| B | Adic | protein | 420 | 63% helix, 0% strand | P60066 |
| C | Adic | protein | 420 | 63% helix, 0% strand | P60066 |
| D | Adic | protein | 419 | 62% helix, 0% strand | P60066 |
| Q | Fab heavy chain | protein | 218 | 3% helix, 39% strand | — |
| P | Fab heavy chain | protein | 219 | 3% helix, 37% strand | — |
| W, S | Fab light chain | protein | 211 | 5% helix, 41% strand | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.79 | 0.99 | 21 | empty |
| 2 | 80 | 0.76 | 0.98 | 21 | empty |
| 3 | 489 | 0.74 | 0.83 | 54 | empty |
| 4 | 531 | 0.73 | 0.81 | 52 | empty |
| 5 | 521 | 0.73 | 0.81 | 50 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2671 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2576 Ų buried · 23 hydrogen bonds · protein-protein
- P–S · 1834 Ų buried · 13 hydrogen bonds · protein-protein
- Q–W · 1807 Ų buried · 12 hydrogen bonds · protein-protein
- B–P · 450 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3NCY · X-ray crystal structure of an arginine agmatine antiporter (AdiC) in complex with a Fab… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P60066 · AlphaFold monomer V2.0 prediction for ARGININE/AGMATINE antiporter (P60066) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P60066
- Elsewhere: RCSB PDB 3NCY · PDBe 3NCY · UniProt P60066
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