Research workbench
Carbon regulatory pii-like protein sbtb from synechocystis sp. 6803 in complex with AMP
Analyse Carbon regulatory pii-like protein sbtb from synechocystis sp. 6803 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O3R
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-associated protein SLR1513
- UniProt
- P73954
- Ligands
- AMP, BCT
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-associated protein SLR1513 | protein | 96 | 33% helix, 45% strand | P73954 |
| B | Membrane-associated protein SLR1513 | protein | 101 | 32% helix, 43% strand | P73954 |
| C | Membrane-associated protein SLR1513 | protein | 99 | 32% helix, 43% strand | P73954 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- BCT · Bicarbonate ion · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.66 | 0.87 | 24 | AMP |
| 2 | 180 | 0.66 | 0.86 | 26 | AMP |
| 3 | 169 | 0.66 | 0.86 | 25 | AMP |
| 4 | 50 | 0.24 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 965 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 938 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 897 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5O3R · Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P73954 · AlphaFold monomer V2.0 prediction for membrane-associated protein SLR1513 (P73954) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P73954
- Elsewhere: RCSB PDB 5O3R · PDBe 5O3R · UniProt P73954
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