MolNFT v1 · #52694 · protein
Crystal structure of spin labeled WZA24-345.
2W8H · Putative outer membrane lipoprotein wza: “Crystal structure of spin labeled WZA24-345.”. X-ray diffraction, 2 ligands (MTN, CL), 20 pockets (best druggability 0.67). MolNFT v1 #52694 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2W8H
- Type
- protein
- Length
- 2,576 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative outer membrane lipoprotein wza
- UniProt
- Q9X4B7
- Ligands
- MTN, CL
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative outer membrane lipoprotein wza | protein | 322 | 21% helix, 31% strand | Q9X4B7 |
Ligands and binding sites
- MTN · S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.67 | 0.82 | 48 | empty |
| 2 | 318 | 0.67 | 0.81 | 44 | empty |
| 3 | 330 | 0.67 | 0.81 | 46 | empty |
| 4 | 330 | 0.66 | 0.81 | 46 | empty |
| 5 | 323 | 0.66 | 0.81 | 46 | empty |
Interfaces
16 interfaces between chains.
- B–F · 3658 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 3644 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3640 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 3637 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3626 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2W8H · Crystal structure of spin labeled Wza24-345. · 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 2W8H · PDBe 2W8H · UniProt Q9X4B7
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