Research workbench
High resolution crystal structure of transmembrane domain of M2
Analyse High resolution crystal structure of transmembrane domain of M2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LBW
- Type
- protein
- Length
- 88 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M2 protein
- UniProt
- Q9YP62
- Ligands
- Z82, XYL, NH2
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | M2 protein | protein | 22 | 91% helix, 0% strand | Q9YP62 |
Ligands and binding sites
- Z82 · 4-bromobenzoic acid · ligand · 4 copies · chains A, B, C, D
- XYL · Xylitol · ligand · chains B
- NH2 · Amino group · ion · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.77 | 0.96 | 25 | empty |
Interfaces
5 interfaces between chains.
- B–C · 487 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 484 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 483 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 480 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3LBW · High resolution crystal structure of transmembrane domain of M2 · 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 Q9YP62
- Elsewhere: RCSB PDB 3LBW · PDBe 3LBW · UniProt Q9YP62
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