Research workbench
Structure of phenoxazinone synthase from streptomyces antibioticus reveals a new type 2 copper center.
Analyse Structure of phenoxazinone synthase from streptomyces antibioticus reveals a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GYR
- Type
- protein
- Length
- 7,044 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenoxazinone synthase
- EC
- 1.-.-.-
- UniProt
- Q53692
- Ligands
- C2O, CU
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Phenoxazinone synthase (EC 1.-.-.-) | protein | 587 | 6% helix, 43% strand | Q53692 |
Ligands and binding sites
- C2O · Cu-O-Cu linkage · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CU · Copper (II) ion · metal · 36 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.76 | 0.98 | 29 | empty |
| 2 | 86 | 0.75 | 0.98 | 32 | empty |
| 3 | 82 | 0.75 | 0.98 | 30 | empty |
| 4 | 83 | 0.75 | 0.98 | 29 | empty |
| 5 | 89 | 0.74 | 0.97 | 28 | empty |
Interfaces
18 interfaces between chains.
- D–L · 2198 Ų buried · 33 hydrogen bonds · protein-protein
- B–H · 2197 Ų buried · 31 hydrogen bonds · protein-protein
- A–I · 2192 Ų buried · 32 hydrogen bonds · protein-protein
- F–J · 2185 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 2162 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3GYR · Structure of Phenoxazi synthase from Streptomyces antibioticus reveals a new type 2… · the same entry in another collection · chain E against E, 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 Q53692
- Elsewhere: RCSB PDB 3GYR · PDBe 3GYR · UniProt Q53692
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