Research workbench
Agmatine deiminase of enterococcus faecalis catalyzing its reaction.
Analyse Agmatine deiminase of enterococcus faecalis catalyzing its reaction. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JER
- Type
- protein
- Length
- 2,935 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatine deiminase
- EC
- 3.5.3.12
- UniProt
- Q837U5
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Agmatine deiminase (EC 3.5.3.12) | protein | 366 | 28% helix, 25% strand | Q837U5 |
| B | Agmatine deiminase (EC 3.5.3.12) | protein | 364 | 28% helix, 25% strand | Q837U5 |
| C, F | Agmatine deiminase (EC 3.5.3.12) | protein | 367 | 27% helix, 25% strand | Q837U5 |
| D | Agmatine deiminase (EC 3.5.3.12) | protein | 372 | 27% helix, 24% strand | Q837U5 |
| E | Agmatine deiminase (EC 3.5.3.12) | protein | 368 | 26% helix, 24% strand | Q837U5 |
| H | Agmatine deiminase (EC 3.5.3.12) | protein | 365 | 27% helix, 25% strand | Q837U5 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.79 | 0.89 | 62 | empty |
| 2 | 197 | 0.73 | 0.90 | 36 | empty |
| 3 | 210 | 0.73 | 0.89 | 40 | empty |
| 4 | 665 | 0.71 | 0.78 | 52 | empty |
| 5 | 163 | 0.69 | 0.89 | 32 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1060 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1029 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1025 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 751 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 2JER · Agmatine deiminase of Enterococcus faecalis catalyzing its reaction. · the same entry in another collection · chain H against H, TM-score 1.00
- Q837U5 · AlphaFold monomer V2.0 prediction for putative agmatine deiminase (Q837U5) · a predicted model of the same protein · chain B 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 Q837U5
- Elsewhere: RCSB PDB 2JER · PDBe 2JER · UniProt Q837U5
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