Research workbench
Cryo-EM structure of the sodium-driven CHLORIDE/BICARBONATE exchanger ndcbe (SLC4A8)
Analyse Cryo-EM structure of the sodium-driven CHLORIDE/BICARBONATE exchanger ndcbe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RTM
- Type
- protein
- Length
- 1,142 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Electroneutral sodium bicarbonate exchanger 1
- Ligands
- NAG, NA, CO3
- Pockets
- 19 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 57% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Electroneutral sodium bicarbonate exchanger 1 | protein | 571 | 57% helix, 3% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.82 | 0.95 | 28 | empty |
| 2 | 536 | 0.73 | 0.81 | 67 | NA, CO3 |
| 3 | 451 | 0.70 | 0.80 | 48 | CO3 |
| 4 | 50 | 0.66 | 0.96 | 24 | empty |
| 5 | 519 | 0.66 | 0.77 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1994 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RTM · Cryo-EM Structure of the Sodium-driven Chloride/Bicarbonate Exchanger NDCBE (SLC4A8) · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7RTM · PDBe 7RTM
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