Research workbench
The soxyz complex of paracoccus pantotrophus
Analyse The soxyz complex of paracoccus pantotrophus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OXH
- Type
- protein
- Length
- 878 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soxz protein; Soxy protein
- UniProt
- Q9LCU8, Q9LCU9
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z, A, C, E | Soxz protein | protein | 107 | 0% helix, 55% strand | Q9LCU8 |
| Y | Soxy protein | protein | 111 | 9% helix, 51% strand | Q9LCU9 |
| B | Soxy protein | protein | 115 | 8% helix, 47% strand | Q9LCU9 |
| D | Soxy protein | protein | 110 | 9% helix, 52% strand | Q9LCU9 |
| F | Soxy protein | protein | 114 | 8% helix, 47% strand | Q9LCU9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains Y, Z, A, B, D, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.74 | 0.80 | 102 | EDO |
| 2 | 157 | 0.58 | 0.83 | 31 | empty |
| 3 | 294 | 0.55 | 0.76 | 48 | EDO |
| 4 | 177 | 0.54 | 0.79 | 29 | empty |
| 5 | 180 | 0.52 | 0.78 | 22 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1216 Ų buried · 31 hydrogen bonds · protein-protein
- Z–Y · 1209 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1119 Ų buried · 29 hydrogen bonds · protein-protein
- Y–B · 610 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2OXH · The SOXYZ Complex of Paracoccus Pantotrophus · the same entry in another collection · chain Z against Z, 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 Q9LCU8
- Every structure of UniProt Q9LCU9
- Elsewhere: RCSB PDB 2OXH · PDBe 2OXH · UniProt Q9LCU8 · UniProt Q9LCU9
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