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Crystal structure of glxr transcription factor from corynebacterium glutamicum with camp
Analyse Crystal structure of glxr transcription factor from corynebacterium glutamicum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R6S
- Type
- protein
- Length
- 1,345 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription regulator
- UniProt
- Q79VI7
- Ligands
- CMP
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Transcription regulator | protein | 225 | 46% helix, 23% strand | Q79VI7 |
| C, D | Transcription regulator | protein | 224 | 46% helix, 26% strand | Q79VI7 |
| F | Transcription regulator | protein | 222 | 43% helix, 27% strand | Q79VI7 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 6 copies · chains A, C, B, D, E, F
- HEZ · Hexane-1,6-diol · additive · 3 copies · chains A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.83 | 0.87 | 69 | CMP |
| 2 | 491 | 0.81 | 0.88 | 58 | CMP |
| 3 | 417 | 0.79 | 0.88 | 52 | CMP |
| 4 | 854 | 0.77 | 0.80 | 55 | CMP |
| 5 | 1106 | 0.73 | 0.77 | 90 | CMP |
Interfaces
10 interfaces between chains.
- A–C · 1872 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1669 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 489 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 260 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 257 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3R6S · Crystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP · the same entry in another collection · chain F against F, TM-score 1.00
- Q79VI7 · AlphaFold monomer V2.0 prediction for crp-like camp-activated global transcriptional… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q79VI7
- Elsewhere: RCSB PDB 3R6S · PDBe 3R6S · UniProt Q79VI7
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