Research workbench
Lytm domain of envc, an activator of cell wall amidases in escherichia COLI
Analyse Lytm domain of envc, an activator of cell wall amidases in escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BH5
- Type
- protein
- Length
- 520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Murein hydrolase activator envc
- UniProt
- P37690
- Ligands
- K, IOD, CL
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Murein hydrolase activator envc | protein | 130 | 2% helix, 48% strand | P37690 |
Ligands and binding sites
- K · Potassium ion · metal · chains A, C
- IOD · Iodide ion · ion · 23 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C, D
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 | 1064 | 0.79 | 0.81 | 90 | IOD, GOL |
| 2 | 161 | 0.42 | 0.74 | 27 | IOD |
Interfaces
6 interfaces between chains.
- B–C · 868 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 660 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 658 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 180 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 102 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4BH5 · LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli · the same entry in another collection · chain D against D, TM-score 1.00
- P37690 · AlphaFold monomer V2.0 prediction for murein hydrolase activator envc (P37690) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P37690
- Elsewhere: RCSB PDB 4BH5 · PDBe 4BH5 · UniProt P37690
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