Research workbench
The escherichia COLI lytic transglycosylase SLT35 in complex with two murodipeptides (glcnac-murnac-L-ala-D-glu)
Analyse The escherichia COLI lytic transglycosylase SLT35 in complex with two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D0K
- Type
- protein
- Length
- 318 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 35KD soluble lytic transglycosylase
- UniProt
- P41052
- Ligands
- AMU, NAG, CA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 35KD soluble lytic transglycosylase | protein | 318 | 51% helix, 11% strand | P41052 |
Ligands and binding sites
- AMU · N-acetyl-beta-muramic acid · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · 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 | 512 | 0.64 | 0.76 | 42 | AMU, NAG, GOL |
| 2 | 51 | 0.31 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 2 covalent, 2 d-amino (covalent ligand, D-amino acid).
Compared structures
- 1D0K · The escherichia COLI lytic transglycosylase SLT35 in complex with two murodipeptides… · the same entry in another collection · chain A against A, TM-score 1.00
- P41052 · AlphaFold monomer V2.0 prediction for membrane-bound lytic murein transglycosylase B… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P41052
- Elsewhere: RCSB PDB 1D0K · PDBe 1D0K · UniProt P41052
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