Research workbench
Crystal structure of putative PEPTIDE:N-glycosidase F (pngase F) (YP_210507.1) from bacteroides fragilis nctc 9343 at 2.30 a resolution
Analyse Crystal structure of putative PEPTIDE:N-glycosidase F (pngase F) (YP_210507.1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KS7
- Type
- protein
- Length
- 1,563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative putative pngase F
- UniProt
- Q5LH31
- Ligands
- CL, IOD
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative putative pngase F | protein | 391 | 9% helix, 44% strand | Q5LH31 |
| B, C | Putative putative pngase F | protein | 390 | 11% helix, 44% strand | Q5LH31 |
| D | Putative putative pngase F | protein | 392 | 10% helix, 44% strand | Q5LH31 |
Ligands and binding sites
- CL · Chloride ion · ion · 10 copies · chains A, B, D, C
- IOD · Iodide ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.60 | 0.77 | 37 | empty |
| 2 | 263 | 0.56 | 0.77 | 38 | IOD |
| 3 | 207 | 0.53 | 0.77 | 30 | CL |
| 4 | 208 | 0.52 | 0.77 | 30 | IOD, EDO |
| 5 | 191 | 0.52 | 0.77 | 30 | CL |
Interfaces
4 interfaces between chains.
- A–B · 1849 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 344 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 5 disulfide (engineered, disulfide).
Compared structures
- 3KS7 · Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from… · 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 Q5LH31
- Elsewhere: RCSB PDB 3KS7 · PDBe 3KS7 · UniProt Q5LH31
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