MolNFT v1 · #124489 · protein
Spin-labeled T4 lysozyme construct I9V1/V131V1 (30 days)
5KGR · Endolysin: “Spin-labeled T4 lysozyme construct I9V1/V131V1 (30 days)”. X-ray diffraction, 3 ligands (K, CL, V1A), 1 pocket (best druggability 0.52). MolNFT v1 #124489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KGR
- 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
- K, CL, V1A
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endolysin (EC 3.2.1.17) | protein | 164 | 65% helix, 8% strand | P00720 |
Ligands and binding sites
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- V1A · S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate · ion · 2 copies · chains A
- HEZ · Hexane-1,6-diol · additive · chains A
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 | 258 | 0.52 | 0.75 | 30 | K |
Compared structures
- 5KGR · Spin-Labeled T4 Lysozyme Construct I9V1/V131V1 (30 days) · 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 5KGR · PDBe 5KGR · UniProt P00720
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