MolNFT v1 · #148615 · protein
The X-ray structure of lytic transglycosylase slt from pseudomonas aeruginosa in complex with the reaction product nag- anhnampentapeptide
6FBT · Lytic murein transglycosylase: “The X-ray structure of lytic transglycosylase slt from pseudomonas aeruginosa in complex with the reaction…”. X-ray diffraction, 5 ligands (DAL, AH0, API), 4 pockets (best druggability 0.49). MolNFT…
- PDB
- 6FBT
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lytic murein transglycosylase; Nag-anhnampentapeptide
- UniProt
- A0A225KQS3
- Ligands
- DAL, AH0, API, NAG, PO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lytic murein transglycosylase | protein | 610 | 66% helix, 1% strand | A0A225KQS3 |
| E | Nag-anhnampentapeptide | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- DAL · D-alanine · ligand · 2 copies · chains A
- AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · chains A, E
- API · 2,6-diaminopimelic acid · ligand · chains A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.49 | 0.77 | 19 | API, DAL |
| 2 | 96 | 0.41 | 0.77 | 17 | empty |
| 3 | 72 | 0.35 | 0.76 | 14 | empty |
| 4 | 74 | 0.31 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–E · 168 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino, 1 disulfide (covalent ligand, D-amino acid, disulfide).
Compared structures
- 6FBT · The X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex… · the same entry in another collection · chain E against E, 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 A0A225KQS3
- Elsewhere: RCSB PDB 6FBT · PDBe 6FBT · UniProt A0A225KQS3
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