Research workbench
Crystal structure of the H233A mutant of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with PREQ0
Analyse Crystal structure of the H233A mutant of 7-cyano-7-deazaguanine reductase, quef… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GHM
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-dependent 7-cyano-7-deazaguanine reductase
- EC
- 1.7.1.13
- UniProt
- Q9KTK0
- Ligands
- PRF, MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 259 | 26% helix, 36% strand | Q9KTK0 |
Ligands and binding sites
- PRF · 7-deaza-7-aminomethyl-guanine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.76 | 0.85 | 53 | PRF, GOL |
| 2 | 55 | 0.48 | 0.86 | 14 | empty |
| 3 | 135 | 0.47 | 0.78 | 29 | empty |
| 4 | 113 | 0.46 | 0.79 | 30 | empty |
| 5 | 88 | 0.44 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2209 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 4GHM · Crystal Structure of the H233A mutant of 7-cyano-7-deazaguanine reductase, QueF from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KTK0 · AlphaFold monomer V2.0 prediction for NADPH-dependent 7-cyano-7-deazaguanine reductase… · a predicted model of the same protein · 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 Q9KTK0
- Elsewhere: RCSB PDB 4GHM · PDBe 4GHM · UniProt Q9KTK0
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