Research workbench
Structure of a C-terminally truncated glycoside hydrolase domain from salmonella typhimurium flgj
Analyse Structure of a C-terminally truncated glycoside hydrolase domain from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DN5
- Type
- protein
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan hydrolase flgj
- EC
- 3.2.1.-
- UniProt
- P15931
- Ligands
- NA, IOD, CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidoglycan hydrolase flgj (EC 3.2.1.-) | protein | 151 | 48% helix, 15% strand | P15931 |
| C | Peptidoglycan hydrolase flgj (EC 3.2.1.-) | protein | 141 | 46% helix, 16% strand | P15931 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- IOD · Iodide ion · ion · 10 copies · chains A, C, B
- CL · Chloride ion · ion · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.75 | 0.87 | 27 | empty |
| 2 | 307 | 0.68 | 0.83 | 53 | NA, IOD |
| 3 | 323 | 0.67 | 0.82 | 59 | IOD |
| 4 | 226 | 0.65 | 0.83 | 44 | IOD |
| 5 | 118 | 0.44 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 764 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 721 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 689 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5DN5 · Structure of a C-terminally truncated glycoside hydrolase domain from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- P15931 · AlphaFold monomer V2.0 prediction for peptidoglycan hydrolase flgj (P15931) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P15931
- Elsewhere: RCSB PDB 5DN5 · PDBe 5DN5 · UniProt P15931
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