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Substrate-bound outward-open state of a na+-coupled sialic acid symporter reveals a novel na+-site
Analyse Substrate-bound outward-open state of a na+-coupled sialic acid symporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NV9
- Type
- protein
- Length
- 480 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative SODIUM:SOLUTE symporter
- UniProt
- B4EZY7
- Ligands
- SLB, NA, PO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative SODIUM:SOLUTE symporter | protein | 480 | 80% helix, 0% strand | B4EZY7 |
Ligands and binding sites
- SLB · N-acetyl-beta-neuraminic acid · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.78 | 0.82 | 55 | SLB |
| 2 | 84 | 0.44 | 0.79 | 15 | empty |
| 3 | 59 | 0.29 | 0.73 | 11 | empty |
| 4 | 50 | 0.27 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 5NV9 · Substrate-bound outward-open state of a Na+-coupled sialic acid symporter reveals a novel… · 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 B4EZY7
- Elsewhere: RCSB PDB 5NV9 · PDBe 5NV9 · UniProt B4EZY7
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