Research workbench
The escherichia COLI lytic transglycosylase SLT35 in complex with bulgecin a and (GLCNAC)2
Analyse The escherichia COLI lytic transglycosylase SLT35 in complex with bulgecin a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D0M
- Type
- protein
- Length
- 312 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 35KD soluble lytic transglycosylase
- UniProt
- P41052
- Ligands
- BLG, NDG, NAG, CA
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 35KD soluble lytic transglycosylase | protein | 312 | 49% helix, 9% strand | P41052 |
Ligands and binding sites
- BLG · 4-O-(4-O-sulfonyl-N-acetylglucosamininyl)-5-methylhydroxy-L-proline-taurine · ligand · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 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 | 358 | 0.57 | 0.75 | 36 | NDG, NAG, BLG |
| 2 | 62 | 0.29 | 0.74 | 17 | empty |
Compared structures
- 1D0M · The escherichia COLI lytic transglycosylase SLT35 in complex with bulgecin a and (GLCNAC)2 · 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 1D0M · PDBe 1D0M · UniProt P41052
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