MolNFT v1 · #149465 · protein
Corynebacterium glutamicum oxyr C206 mutant
6G1D · Hydrogen peroxide-inducible genes activator: “Corynebacterium glutamicum oxyr C206 mutant”. X-ray diffraction, 3 ligands (FOR, NA, SO4), 12 pockets (best druggability 0.81). MolNFT v1 #149465 on GenesisL1: 3D structure, binding…
- PDB
- 6G1D
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogen peroxide-inducible genes activator
- UniProt
- A0A2H5I9R9
- Ligands
- FOR, NA, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Hydrogen peroxide-inducible genes activator | protein | 310 | 47% helix, 20% strand | A0A2H5I9R9 |
| D | Hydrogen peroxide-inducible genes activator | protein | 318 | 46% helix, 20% strand | A0A2H5I9R9 |
| B | Hydrogen peroxide-inducible genes activator | protein | 313 | 47% helix, 20% strand | A0A2H5I9R9 |
| A | Hydrogen peroxide-inducible genes activator | protein | 315 | 46% helix, 19% strand | A0A2H5I9R9 |
Ligands and binding sites
- FOR · Formyl group · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains C, D, B, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains C, D, B, A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, A, D
- FMT · Formic acid · additive · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.81 | 0.83 | 104 | empty |
| 2 | 215 | 0.71 | 0.88 | 35 | empty |
| 3 | 572 | 0.63 | 0.75 | 50 | empty |
| 4 | 376 | 0.59 | 0.76 | 40 | empty |
| 5 | 231 | 0.58 | 0.79 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1711 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 1245 Ų buried · 22 hydrogen bonds · protein-protein
- D–B · 1231 Ų buried · 21 hydrogen bonds · protein-protein
- C–B · 224 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6G1D · Corynebacterium glutamicum OxyR C206 mutant · the same entry in another collection · chain C against C, 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 A0A2H5I9R9
- Elsewhere: RCSB PDB 6G1D · PDBe 6G1D · UniProt A0A2H5I9R9
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