MolNFT v1 · #90484 · protein
T4 lysozyme L99A/M102H with 2-cyanophenol bound
4EKR: “T4 lysozyme L99A/M102H with 2-cyanophenol bound”. X-ray diffraction, 2 ligands (0R0, SO4), 2 pockets (best druggability 0.72). MolNFT v1 #90484 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4EKR
- Type
- protein
- Length
- 349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- 0R0, SO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 175 | 65% helix, 9% strand | P00720 |
| B | Lysozyme (EC 3.2.1.17) | protein | 174 | 66% helix, 9% strand | P00720 |
Ligands and binding sites
- 0R0 · 2-hydroxybenzonitrile · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
- HED · 2-hydroxyethyl disulfide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.72 | 0.77 | 60 | ACT |
| 2 | 189 | 0.49 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (additive adduct, disulfide).
Compared structures
- 4EKR · T4 Lysozyme L99A/M102H with 2-Cyanophenol Bound · 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 4EKR · PDBe 4EKR · UniProt P00720
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