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Crystal structure of arginine deiminase from group a streptococcus
Analyse Crystal structure of arginine deiminase from group a streptococcus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BOF
- Type
- protein
- Length
- 3,268 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine deiminase
- EC
- 3.5.3.6
- UniProt
- P0C0B3
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, H | Arginine deiminase (EC 3.5.3.6) | protein | 408 | 35% helix, 22% strand | P0C0B3 |
| B | Arginine deiminase (EC 3.5.3.6) | protein | 411 | 33% helix, 22% strand | P0C0B3 |
| C, D, F | Arginine deiminase (EC 3.5.3.6) | protein | 409 | 36% helix, 21% strand | P0C0B3 |
| E | Arginine deiminase (EC 3.5.3.6) | protein | 406 | 34% helix, 22% strand | P0C0B3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, H, B, C, D, E, F, G
- PGE · Triethylene glycol · additive · 2 copies · chains A, F
- PG4 · Tetraethylene glycol · additive · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.79 | 0.81 | 90 | PG4 |
| 2 | 853 | 0.77 | 0.81 | 94 | empty |
| 3 | 840 | 0.74 | 0.78 | 70 | empty |
| 4 | 1159 | 0.72 | 0.76 | 74 | empty |
| 5 | 605 | 0.72 | 0.80 | 76 | empty |
Interfaces
14 interfaces between chains.
- A–H · 1385 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1383 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1365 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 379 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 333 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P0C0B3
- Elsewhere: RCSB PDB 4BOF · PDBe 4BOF · UniProt P0C0B3
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