MolNFT v1 · #55020 · protein
The structure of cymr (yrzc) the global cysteine regulator of B. subtilis
2Y75 · Hth-type transcriptional regulator cymr: “The structure of cymr (yrzc) the global cysteine regulator of B. subtilis”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.81). MolNFT v1 #55020 on GenesisL1: 3D…
- 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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