Research workbench
Cryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB from Synechocystis sp. PCC 6803
Analyse Cryo-EM structure of bicarbonate transporter SbtA in complex with PII-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CYF
- Type
- protein
- Length
- 1,329 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.15
- Source
- Synechocystis sp. PCC 6803 substr. Kazusa
- Molecule
- Slr1512 protein; Membrane-associated protein slr1513
- UniProt
- P73953, P73954
- Ligands
- AMP, NA
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · resolution 3.15 · 2 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Slr1512 protein | protein | 334 | 63% helix, 0% strand | P73953 |
| D, E, F | Membrane-associated protein slr1513 | protein | 109 | 24% helix, 37% strand | P73954 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C
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 | 977 | 0.87 | 0.88 | 126 | empty |
| 2 | 241 | 0.86 | 0.97 | 25 | empty |
| 3 | 181 | 0.74 | 0.91 | 29 | AMP |
| 4 | 182 | 0.73 | 0.90 | 32 | AMP |
| 5 | 190 | 0.71 | 0.89 | 34 | AMP |
Interfaces
12 interfaces between chains.
- B–C · 1005 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1004 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1003 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 937 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 918 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7CYF · Cryo-EM structure of bicarbonate transporter sbta in complex with pii- like signaling… · 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 7CYF · PDBe 7CYF · UniProt P73953 · UniProt P73954
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