MolNFT v1 · #177375 · protein
Bicarbonate transporter complex sbta-sbtb bound to AMP
7EGK · Sodium-dependent bicarbonate transporter sbta: “Bicarbonate transporter complex sbta-sbtb bound to AMP”. Electron microscopy, 2 ligands (AMP, NA), 14 pockets (best druggability 0.87). MolNFT v1 #177375 on GenesisL1: 3D structure…
- PDB
- 7EGK
- Type
- protein
- Length
- 1,317 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent bicarbonate transporter sbta; Membrane-associated protein sbtb
- UniProt
- P73953, P73954
- Ligands
- AMP, NA
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 65% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Sodium-dependent bicarbonate transporter sbta | protein | 330 | 76% helix, 0% strand | P73953 |
| D, F, B | Membrane-associated protein sbtb | protein | 109 | 31% helix, 38% strand | P73954 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains D, F, B
- NA · Sodium ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.87 | 0.88 | 127 | empty |
| 2 | 285 | 0.86 | 0.96 | 24 | empty |
| 3 | 187 | 0.78 | 0.93 | 30 | AMP |
| 4 | 181 | 0.77 | 0.93 | 28 | AMP |
| 5 | 186 | 0.76 | 0.92 | 29 | AMP |
Interfaces
12 interfaces between chains.
- C–E · 1008 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1007 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1006 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 935 Ų buried · 14 hydrogen bonds · protein-protein
- D–B · 935 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EGK · Bicarbonate transporter complex SbtA-SbtB bound to AMP · the same entry in another collection · chain C against C, TM-score 1.00
- P73954 · AlphaFold monomer V2.0 prediction for membrane-associated protein SLR1513 (P73954) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P73953
- Every structure of UniProt P73954
- Elsewhere: RCSB PDB 7EGK · PDBe 7EGK · UniProt P73953 · UniProt P73954
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