MolNFT v1 · #148650 · protein
The X-ray structure of lytic transglycosylase slt inactive mutant E503Q from pseudomonas aeruginosa in complex with nag- nampentapeptide-nag-nampentapeptide
6FCS · Soluble lytic murein transglycosylase: “The X-ray structure of lytic transglycosylase slt inactive mutant E503Q from pseudomonas aeruginosa in…”. X-ray diffraction, 7 ligands (API, AMU, AMV), 7 pockets (best druggability 0.42).…
- PDB
- 6FCS
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble lytic murein transglycosylase; Ala-dgl-api-dal-dal
- EC
- 4.2.2.-
- UniProt
- A0A069QJX4
- Ligands
- API, AMU, AMV, NM6, 66N, NAG, MAG
- Pockets
- 7 · best druggability 0.42
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 |
| B | Ala-dgl-api-dal-dal | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · chains A, B
- AMU · N-acetyl-beta-muramic acid · ligand · chains A
- AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · chains A, B
- NM6 · 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranose · ligand · chains A
- 66N · L-alaninamide · ligand
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAG · methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · sugar · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.42 | 0.77 | 16 | API |
| 2 | 112 | 0.41 | 0.76 | 17 | empty |
| 3 | 90 | 0.41 | 0.78 | 17 | AMV, NAG |
| 4 | 70 | 0.35 | 0.76 | 15 | empty |
| 5 | 69 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 321 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 d-amino, 1 disulfide (covalent ligand, D-amino acid, disulfide).
Compared structures
- 6FCS · The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas… · the same entry in another collection · chain A against A, 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 6FCS · PDBe 6FCS · UniProt A0A069QJX4
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