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
- 2OX5
- Type
- protein
- Length
- 870 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soxz protein; Soxy protein
- UniProt
- Q9LCU8, Q9LCU9
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z, A | Soxz protein | protein | 108 | 0% helix, 58% strand | Q9LCU8 |
| Y | Soxy protein | protein | 113 | 9% helix, 53% strand | Q9LCU9 |
| B | Soxy protein | protein | 111 | 9% helix, 51% strand | Q9LCU9 |
| C | Soxz protein | protein | 103 | 0% helix, 59% strand | Q9LCU8 |
| D | Soxy protein | protein | 113 | 8% helix, 53% strand | Q9LCU9 |
| E | Soxz protein | protein | 101 | 0% helix, 56% strand | Q9LCU8 |
| F | Soxy protein | protein | 113 | 8% helix, 51% strand | Q9LCU9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains Y, D, A, B
- ACT · Acetate ion · additive · 8 copies · chains Z, A, B, D, E, F
- EDO · 1,2-ethanediol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.73 | 0.79 | 79 | SO4 |
| 2 | 1061 | 0.71 | 0.75 | 91 | ACT |
| 3 | 351 | 0.61 | 0.78 | 55 | empty |
| 4 | 163 | 0.47 | 0.77 | 20 | empty |
| 5 | 132 | 0.46 | 0.78 | 20 | ACT |
Interfaces
13 interfaces between chains.
- Z–Y · 1213 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1127 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1022 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 689 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered, artifact).
Compared structures
- 2OX5 · 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 2OX5 · PDBe 2OX5 · UniProt Q9LCU8 · UniProt Q9LCU9
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