Research workbench
The structure of cymr (yrzc) the global cysteine regulator of B. subtilis
Analyse The structure of cymr (yrzc) the global cysteine regulator of B. subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y75
- Type
- protein
- Length
- 765 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator cymr
- UniProt
- O34527
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator cymr | protein | 125 | 58% helix, 10% strand | O34527 |
| B | Hth-type transcriptional regulator cymr | protein | 127 | 57% helix, 11% strand | O34527 |
| C | Hth-type transcriptional regulator cymr | protein | 127 | 57% helix, 11% strand | O34527 |
| D | Hth-type transcriptional regulator cymr | protein | 128 | 56% helix, 11% strand | O34527 |
| E, F | Hth-type transcriptional regulator cymr | protein | 129 | 57% helix, 12% strand | O34527 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, C, E, B, F, D
- CL · Chloride ion · ion · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.81 | 0.87 | 60 | SO4 |
| 2 | 175 | 0.68 | 0.87 | 30 | empty |
| 3 | 194 | 0.65 | 0.84 | 29 | empty |
| 4 | 134 | 0.64 | 0.87 | 32 | empty |
| 5 | 107 | 0.59 | 0.85 | 18 | SO4 |
Interfaces
12 interfaces between chains.
- E–F · 2020 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2016 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1973 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 391 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2Y75 · The Structure of CymR (YrzC) the Global Cysteine Regulator of B. subtilis · the same entry in another collection · chain F against F, TM-score 1.00
- O34527 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator cymr (O34527) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 O34527
- Elsewhere: RCSB PDB 2Y75 · PDBe 2Y75 · UniProt O34527
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