Research workbench
Backbone modifications in the protein GB1 helix: AIB24, beta-3-LYS28, beta-3-LYS31, AIB35
Analyse Backbone modifications in the protein GB1 helix: AIB24, 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
- 5HI1
- Type
- protein
- Length
- 448 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein G
- UniProt
- P19909
- Ligands
- NH2
- Pockets
- 3 · best druggability 0.77
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 | Immunoglobulin G-binding protein G | protein | 56 | 25% helix, 43% strand | P19909 |
Ligands and binding sites
- NH2 · Amino group · ion · 8 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · 2 copies · chains C, G, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.77 | 0.81 | 88 | empty |
| 2 | 262 | 0.70 | 0.85 | 36 | empty |
| 3 | 262 | 0.60 | 0.80 | 32 | empty |
Interfaces
16 interfaces between chains.
- C–E · 523 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 305 Ų buried · 3 hydrogen bonds · protein-protein
- D–H · 268 Ų buried · 8 hydrogen bonds · protein-protein
- F–H · 266 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 265 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (nonstandard).
Compared structures
- 5HI1 · Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 · the same entry in another collection · chain B against B, TM-score 0.99
- P19909 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P19909) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P19909
- Elsewhere: RCSB PDB 5HI1 · PDBe 5HI1 · UniProt P19909
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