MolNFT v1 · #175897 · protein
Spua mutant - H221N with glu
7D53 · Probable glutamine amidotransferase: “Spua mutant - H221N with glu”. X-ray diffraction, 2 ligands (GLU, MG), 7 pockets (best druggability 0.74). MolNFT v1 #175897 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7D53
- Type
- protein
- Length
- 992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable glutamine amidotransferase
- UniProt
- Q9I6J4
- Ligands
- GLU, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Probable glutamine amidotransferase | protein | 249 | 33% helix, 24% strand | Q9I6J4 |
| B | Probable glutamine amidotransferase | protein | 246 | 35% helix, 24% strand | Q9I6J4 |
| C | Probable glutamine amidotransferase | protein | 248 | 34% helix, 24% strand | Q9I6J4 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.74 | 0.79 | 70 | empty |
| 2 | 392 | 0.66 | 0.79 | 53 | empty |
| 3 | 402 | 0.63 | 0.78 | 56 | GLU |
| 4 | 268 | 0.61 | 0.80 | 38 | GLU |
| 5 | 188 | 0.49 | 0.76 | 38 | GLU |
Interfaces
5 interfaces between chains.
- A–B · 1579 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 153 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7D53 · SpuA mutant - H221N with Glu · the same entry in another collection · 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 Q9I6J4
- Elsewhere: RCSB PDB 7D53 · PDBe 7D53 · UniProt Q9I6J4
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