MolNFT v1 · #71414 · protein
Structure of glutamine aminotransferase class-II domain protein (SPO2029) from silicibacter pomeroyi
3MDN: “Structure of glutamine aminotransferase class-II domain protein (SPO2029) from silicibacter pomeroyi”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #71414 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3MDN
- Type
- protein
- Length
- 871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine aminotransferase class-II domain protein
- UniProt
- Q5LRU5
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine aminotransferase class-II domain protein | protein | 218 | 27% helix, 37% strand | Q5LRU5 |
| B | Glutamine aminotransferase class-II domain protein | protein | 214 | 28% helix, 36% strand | Q5LRU5 |
| C | Glutamine aminotransferase class-II domain protein | protein | 216 | 26% helix, 37% strand | Q5LRU5 |
| D | Glutamine aminotransferase class-II domain protein | protein | 223 | 25% helix, 35% strand | Q5LRU5 |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.75 | 0.78 | 83 | empty |
| 2 | 74 | 0.40 | 0.79 | 19 | empty |
| 3 | 56 | 0.34 | 0.77 | 12 | empty |
| 4 | 57 | 0.33 | 0.77 | 15 | empty |
| 5 | 54 | 0.30 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 899 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 891 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 655 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 623 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 177 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3MDN · Structure of glutamine aminotransferase class-II domain protein (SPO2029) from… · the same entry in another collection · chain B against B, 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 Q5LRU5
- Elsewhere: RCSB PDB 3MDN · PDBe 3MDN · UniProt Q5LRU5
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