MolNFT v1 · #47401 · protein
The soxyz complex of paracoccus pantotrophus
2OXG · Soxz protein: “The soxyz complex of paracoccus pantotrophus”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.69). MolNFT v1 #47401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2OXG
- Type
- protein
- Length
- 861 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
- 7 · best druggability 0.69
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z, A | Soxz protein | protein | 108 | 0% helix, 58% strand | Q9LCU8 |
| Y | Soxy protein | protein | 112 | 9% helix, 54% strand | Q9LCU9 |
| B | Soxy protein | protein | 110 | 9% helix, 45% strand | Q9LCU9 |
| C | Soxz protein | protein | 101 | 0% helix, 58% strand | Q9LCU8 |
| D | Soxy protein | protein | 111 | 7% helix, 54% strand | Q9LCU9 |
| E | Soxz protein | protein | 99 | 0% helix, 58% strand | Q9LCU8 |
| F | Soxy protein | protein | 112 | 8% helix, 52% strand | Q9LCU9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains Z, A, Y, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains Z, Y, A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.69 | 0.78 | 69 | empty |
| 2 | 869 | 0.69 | 0.75 | 72 | empty |
| 3 | 122 | 0.51 | 0.81 | 28 | empty |
| 4 | 205 | 0.51 | 0.77 | 26 | empty |
| 5 | 172 | 0.50 | 0.78 | 24 | empty |
Interfaces
13 interfaces between chains.
- Z–Y · 1190 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1177 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1109 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1055 Ų buried · 35 hydrogen bonds · protein-protein
- B–F · 668 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2OXG · 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 2OXG · PDBe 2OXG · UniProt Q9LCU8 · UniProt Q9LCU9
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