MolNFT v1 · #123235 · protein
Structure of spin-labelled T4 lysozyme mutant L118C-R1 at 100K
5JDT · Endolysin: “Structure of spin-labelled T4 lysozyme mutant L118C-R1 at 100K”. X-ray diffraction, 4 ligands (MTN, K, CL), 2 pockets (best druggability 0.62). MolNFT v1 #123235 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5JDT
- Type
- protein
- Length
- 164 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endolysin
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- MTN, K, CL, AZI
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endolysin (EC 3.2.1.17) | protein | 164 | 60% 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 · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- AZI · Azide ion · ion · 2 copies · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.62 | 0.84 | 24 | MTN |
| 2 | 265 | 0.55 | 0.76 | 32 | K |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5JDT · Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K · 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 5JDT · PDBe 5JDT · UniProt P00720
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