Research workbench
X-ray structure of putative agmatine deiminase Q8DW17, northeast structural genomics target SMR6.
Analyse X-ray structure of putative agmatine deiminase Q8DW17, northeast structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EWO
- Type
- protein
- Length
- 4,351 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative agmatine deiminase
- EC
- 3.5.3.12
- UniProt
- Q8DW17
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I, J, K, L | Putative agmatine deiminase (EC 3.5.3.12) | protein | 362 | 26% helix, 25% strand | Q8DW17 |
| H | Putative agmatine deiminase (EC 3.5.3.12) | protein | 369 | 26% helix, 23% strand | Q8DW17 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.85 | 0.87 | 92 | empty |
| 2 | 855 | 0.84 | 0.86 | 93 | empty |
| 3 | 849 | 0.84 | 0.86 | 89 | empty |
| 4 | 813 | 0.75 | 0.79 | 91 | empty |
| 5 | 51 | 0.70 | 0.98 | 22 | empty |
Interfaces
22 interfaces between chains.
- D–I · 902 Ų buried · 9 hydrogen bonds · protein-protein
- E–K · 901 Ų buried · 9 hydrogen bonds · protein-protein
- C–J · 890 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 888 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 872 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 modified (engineered).
Compared structures
- 2EWO · X-ray structure of putative agmatine deiminase Q8DW17, Northeast Structural Genomics… · the same entry in another collection · chain L against L, 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 Q8DW17
- Elsewhere: RCSB PDB 2EWO · PDBe 2EWO · UniProt Q8DW17
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