Research workbench
Crystal structure of a computationally optimized PG9 mutant
Analyse Crystal structure of a computationally optimized PG9 mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YAQ
- Type
- protein
- Length
- 906 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PG9_N100FY Fab heavy chain; PG9_N100FY light chain
- UniProt
- A0A087X1C7, Q6GMW3
- Ligands
- NAG, FUC, PO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | PG9_N100FY Fab heavy chain | protein | 239 | 6% helix, 54% strand | A0A087X1C7 |
| L, B | PG9_N100FY light chain | protein | 214 | 7% helix, 50% strand | Q6GMW3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains L, A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains L, A, B
- PO4 · Phosphate ion · ion · 2 copies · chains H, L, A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.82 | 0.83 | 101 | empty |
| 2 | 359 | 0.60 | 0.77 | 40 | PO4 |
| 3 | 163 | 0.56 | 0.82 | 29 | empty |
| 4 | 105 | 0.51 | 0.82 | 29 | empty |
| 5 | 258 | 0.50 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1917 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1890 Ų buried · 17 hydrogen bonds · protein-protein
- L–A · 1072 Ų buried · 10 hydrogen bonds · protein-protein
- L–B · 220 Ų buried · 2 hydrogen bonds · protein-protein
- H–B · 201 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 modified, 2 glycan (disulfide, sulfation, N-glycosylation, cyclization).
Compared structures
- 4YAQ · Crystal structure of a computationally optimized PG9 mutant · the same entry in another collection · chain H against H, 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 A0A087X1C7
- Every structure of UniProt Q6GMW3
- Elsewhere: RCSB PDB 4YAQ · PDBe 4YAQ · UniProt A0A087X1C7 · UniProt Q6GMW3
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