Research workbench
Structure of spin-labeled T4 lysozyme mutant S44R1
Analyse Structure of spin-labeled T4 lysozyme mutant S44R1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q9E
- Type
- protein
- Length
- 492 residues
- Chains
- 3
- Method
- x-ray diffraction; epr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- MTN
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction; epr · 1 distinct chain · 64% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lysozyme (EC 3.2.1.17) | protein | 164 | 64% helix, 8% strand | P00720 |
Ligands and binding sites
- MTN · S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate · ligand · 3 copies · chains A, B, C
- HED · 2-hydroxyethyl disulfide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.63 | 0.78 | 44 | empty |
| 2 | 109 | 0.56 | 0.84 | 23 | empty |
| 3 | 288 | 0.54 | 0.76 | 30 | empty |
| 4 | 150 | 0.51 | 0.79 | 18 | MTN |
| 5 | 170 | 0.48 | 0.77 | 21 | HED |
Interfaces
3 interfaces between chains.
- B–C · 755 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 281 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 174 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2Q9E · Structure of spin-labeled T4 lysozyme mutant S44R1 · 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 P00720
- Elsewhere: RCSB PDB 2Q9E · PDBe 2Q9E · UniProt P00720
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