MolNFT v1 · #40834 · protein
The structure of wza
2J58 · Outer membrane lipoprotein wza: “The structure of wza”. X-ray diffraction, 2 ligands (SC2, SO4), 20 pockets (best druggability 0.70). MolNFT v1 #40834 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J58
- Type
- protein
- Length
- 2,846 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane lipoprotein wza
- UniProt
- Q9X4B7
- Ligands
- SC2, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Outer membrane lipoprotein wza | protein | 355 | 28% helix, 29% strand | Q9X4B7 |
| B, C, D, E, G, H | Outer membrane lipoprotein wza | protein | 356 | 28% helix, 29% strand | Q9X4B7 |
Ligands and binding sites
- SC2 · N-acetyl-L-cysteine · ligand · 2 copies · chains A, E, F
- SO4 · Sulfate ion · ion · 16 copies · chains A, D, B, C, H, E, F, G
- OCT · N-octane · additive · 8 copies · chains A, B, G, C, F, D, E, H
- HEX · Hexane · additive · 8 copies · chains A, B, G, C, F, D, E, H
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 | 432 | 0.70 | 0.81 | 50 | SO4 |
| 2 | 407 | 0.70 | 0.81 | 46 | SO4 |
| 3 | 424 | 0.69 | 0.81 | 44 | SO4 |
| 4 | 576 | 0.67 | 0.77 | 73 | empty |
| 5 | 587 | 0.66 | 0.76 | 67 | empty |
Interfaces
28 interfaces between chains.
- A–D · 4530 Ų buried · 47 hydrogen bonds · protein-protein
- D–E · 4528 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 4495 Ų buried · 53 hydrogen bonds · protein-protein
- C–F · 4492 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 4475 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 86 modified (engineered, nonstandard).
Compared structures
- 2J58 · The structure of Wza · the same entry in another collection · chain A against A, 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 Q9X4B7
- Elsewhere: RCSB PDB 2J58 · PDBe 2J58 · UniProt Q9X4B7
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