MolNFT v1 · #19231 · protein
2.1 a resolution structure of escherichia COLI lytic transglycosylase SLT35
1QDR · Lytic murein transglycosylase B: “2.1 a resolution structure of escherichia COLI lytic transglycosylase SLT35”. X-ray diffraction, 2 ligands (BCN, NA), 3 pockets (best druggability 0.52). MolNFT v1 #19231 on GenesisL1: 3D structure…
- PDB
- 1QDR
- Type
- protein
- Length
- 312 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lytic murein transglycosylase B
- EC
- 3.2.1.-
- UniProt
- P41052
- Ligands
- BCN, NA
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lytic murein transglycosylase B (EC 3.2.1.-) | protein | 312 | 52% helix, 11% strand | P41052 |
Ligands and binding sites
- BCN · Bicine · ligand · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.52 | 0.74 | 35 | BCN, EDO |
| 2 | 53 | 0.32 | 0.77 | 13 | empty |
| 3 | 56 | 0.28 | 0.74 | 18 | empty |
Compared structures
- 1QDR · 2.1 a resolution structure of escherichia COLI lytic transglycosylase SLT35 · 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 0.95
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 1QDR · PDBe 1QDR · UniProt P41052
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