Research workbench
Backbone modifications in the protein GB1 helix: beta-3-ALA24, beta-3- LYS28, beta-3-LYS31, beta-3-ASN35
Analyse Backbone modifications in the protein GB1 helix: beta-3-ALA24, beta-3- LYS28… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KGR
- Type
- protein
- Length
- 448 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptococcal protein GB1 backbone modified variant: beta- 3-ALA24, beta-3-LYS28…
- Ligands
- NH2
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Streptococcal protein GB1 backbone modified variant: beta- 3-ALA24, beta-3-LYS28, beta-3-LYS31, beta-3-ASN35 | protein | 56 | 25% helix, 43% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.54 | 0.76 | 27 | empty |
| 2 | 197 | 0.49 | 0.76 | 35 | empty |
| 3 | 211 | 0.45 | 0.73 | 34 | empty |
| 4 | 57 | 0.36 | 0.78 | 19 | empty |
| 5 | 77 | 0.36 | 0.76 | 18 | empty |
Interfaces
12 interfaces between chains.
- F–G · 514 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 446 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 428 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 317 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 279 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (nonstandard).
Compared structures
- 4KGR · Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28… · the same entry in another collection · chain C against C, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4KGR · PDBe 4KGR
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