Research workbench
Crystal structure of SODIUM/ALANINE symporter agcs with D-alanine bound
Analyse Crystal structure of SODIUM/ALANINE symporter agcs with D-alanine bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CSF
- Type
- protein
- Length
- 1,713 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody Fab heavy chain; Monoclonal antibody Fab light chain; SODIUM/ALANINE…
- UniProt
- Q6LX42
- Ligands
- DAL, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Monoclonal antibody Fab heavy chain | protein | 214 | 3% helix, 50% strand | — |
| B, L | Monoclonal antibody Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| M | SODIUM/ALANINE symporter agcs | protein | 431 | 77% helix, 1% strand | Q6LX42 |
| C | SODIUM/ALANINE symporter agcs | protein | 428 | 77% helix, 1% strand | Q6LX42 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.80 | 0.91 | 44 | empty |
| 2 | 277 | 0.79 | 0.91 | 40 | empty |
| 3 | 610 | 0.77 | 0.83 | 101 | empty |
| 4 | 445 | 0.74 | 0.84 | 67 | empty |
| 5 | 655 | 0.65 | 0.75 | 62 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1728 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1721 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 946 Ų buried · 3 hydrogen bonds · protein-protein
- M–H · 694 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 644 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6CSF · Crystal structure of sodium/alanine symporter AgcS with D-alanine bound · the same entry in another collection · chain L against L, TM-score 1.00
- Q6LX42 · AlphaFold monomer V2.0 prediction for SODIUM/ALANINE symporter agcs (Q6LX42) · a predicted model of the same protein · chain M 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 Q6LX42
- Elsewhere: RCSB PDB 6CSF · PDBe 6CSF · UniProt Q6LX42
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