Research workbench
Crystal structure of SLTB3 from pseudomonas aeruginosa in complex with nag-nam-pentapeptide
Analyse Crystal structure of SLTB3 from pseudomonas aeruginosa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AO8
- Type
- protein
- Length
- 374 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble lytic tranglycosilase B3
- UniProt
- Q9HX28
- Ligands
- NM9, NAG, CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble lytic tranglycosilase B3 | protein | 374 | 51% helix, 6% strand | Q9HX28 |
Ligands and binding sites
- NM9 · methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranoside · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.73 | 0.82 | 41 | empty |
| 2 | 111 | 0.46 | 0.79 | 18 | empty |
| 3 | 111 | 0.43 | 0.77 | 23 | empty |
| 4 | 132 | 0.38 | 0.73 | 28 | NAG |
| 5 | 51 | 0.28 | 0.75 | 10 | empty |
Compared structures
- 5AO8 · Crystal Structure of SltB3 from Pseudomonas aeruginosa in complex with… · 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 Q9HX28
- Elsewhere: RCSB PDB 5AO8 · PDBe 5AO8 · UniProt Q9HX28
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