MolNFT v1 · #135921 · protein
Mutant E97Q crystal structure of bacillus subtilis quef with a disulfide cys 55-99
5UDG · NADPH-dependent 7-cyano-7-deazaguanine reductase: “Mutant E97Q crystal structure of bacillus subtilis quef with a disulfide cys 55-99”. X-ray diffraction, 1 ligand (MG), 17 pockets (best druggability 0.76). MolNFT v1 #135921 on…
- PDB
- 5UDG
- Type
- protein
- Length
- 725 residues
- Chains
- 5
- 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
- A0A063X9I2
- Ligands
- MG
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 145 | 25% helix, 32% strand | A0A063X9I2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, D, E
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.76 | 0.85 | 39 | empty |
| 2 | 539 | 0.75 | 0.82 | 41 | empty |
| 3 | 459 | 0.75 | 0.84 | 43 | empty |
| 4 | 460 | 0.75 | 0.83 | 40 | empty |
| 5 | 366 | 0.72 | 0.84 | 41 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1486 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1484 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1460 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1448 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 1430 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5UDG · Mutant E97Q crystal structure of Bacillus subtilis QueF with a disulfide Cys 55-99 · 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 A0A063X9I2
- Elsewhere: RCSB PDB 5UDG · PDBe 5UDG · UniProt A0A063X9I2
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