Research workbench
Carbon regulatory pii-like protein sbtb from synechocystis sp. 6803 in complex with cyclic di-AMP (C-di-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
- 7OBJ
- Type
- protein
- Length
- 303 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-associated protein SLR1513
- UniProt
- P73954
- Ligands
- 2BA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-associated protein SLR1513 | protein | 100 | 32% helix, 39% strand | P73954 |
| B | Membrane-associated protein SLR1513 | protein | 103 | 31% helix, 41% strand | P73954 |
| C | Membrane-associated protein SLR1513 | protein | 100 | 32% helix, 41% strand | P73954 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.68 | 0.86 | 27 | empty |
| 2 | 265 | 0.64 | 0.81 | 29 | 2BA |
| 3 | 253 | 0.63 | 0.81 | 28 | 2BA |
| 4 | 50 | 0.30 | 0.76 | 16 | empty |
| 5 | 55 | 0.27 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 934 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 893 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7OBJ · Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with… · 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 0.88
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 7OBJ · PDBe 7OBJ · UniProt P73954
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