MolNFT v1 · #148649 · protein
The X-ray structure of lytic transglycosylase slt inactive mutant E503Q from pseudomonas aeruginosa in complex with nag- namtetrapeptide-nag-anhnamtetrapeptide
6FCR · Soluble lytic murein transglycosylase: “The X-ray structure of lytic transglycosylase slt inactive mutant E503Q from pseudomonas aeruginosa in…”. X-ray diffraction, 5 ligands (API, DAL, AMU), 5 pockets (best druggability 0.46).…
- PDB
- 6FCR
- Type
- protein
- Length
- 617 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble lytic murein transglycosylase; Ala-dgl-api-dal
- EC
- 4.2.2.-
- UniProt
- A0A069QJX4
- Ligands
- API, DAL, AMU, AH0, NAG
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble lytic murein transglycosylase (EC 4.2.2.-) | protein | 613 | 68% helix, 1% strand | A0A069QJX4 |
| F, G | Ala-dgl-api-dal | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · 2 copies · chains A, F, G
- DAL · D-alanine · ligand · 2 copies · chains F, A, G
- AMU · N-acetyl-beta-muramic acid · ligand · chains A, F
- AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · chains A, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, F
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.46 | 0.76 | 30 | NAG, AMU, AH0 |
| 2 | 127 | 0.45 | 0.77 | 18 | API, DAL |
| 3 | 141 | 0.40 | 0.74 | 18 | API |
| 4 | 116 | 0.38 | 0.74 | 23 | empty |
| 5 | 61 | 0.33 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–G · 184 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 174 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 d-amino, 1 disulfide (covalent ligand, D-amino acid, disulfide).
Compared structures
- 6FCR · The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas… · the same entry in another collection · chain F against F, 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 A0A069QJX4
- Elsewhere: RCSB PDB 6FCR · PDBe 6FCR · UniProt A0A069QJX4
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