Research workbench
Strcutrue of the full-length ccmr complexed with 2-og from synechocystis PCC6803
Analyse Strcutrue of the full-length ccmr complexed with 2-og from synechocystis PCC6803 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2V
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco operon transcriptional regulator
- UniProt
- P73862
- Ligands
- AKG, PO4
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rubisco operon transcriptional regulator | protein | 304 | 44% helix, 25% strand | P73862 |
| B | Rubisco operon transcriptional regulator | protein | 303 | 44% helix, 23% strand | P73862 |
| C | Rubisco operon transcriptional regulator | protein | 299 | 43% helix, 24% strand | P73862 |
| D | Rubisco operon transcriptional regulator | protein | 302 | 44% helix, 23% strand | P73862 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains B, C, A, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.75 | 0.80 | 70 | PO4, AKG |
| 2 | 771 | 0.74 | 0.80 | 58 | empty |
| 3 | 504 | 0.72 | 0.81 | 66 | AKG, PO4 |
| 4 | 497 | 0.71 | 0.81 | 50 | empty |
| 5 | 419 | 0.68 | 0.80 | 41 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2114 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 2038 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1796 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1721 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 123 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Y2V · Strcutrue of the full-length CcmR complexed with 2-OG from Synechocystis PCC6803 · the same entry in another collection · chain A against A, 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
- Every structure of UniProt P73862
- Elsewhere: RCSB PDB 5Y2V · PDBe 5Y2V · UniProt P73862
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