Research workbench
Backbone modifications in the protein GB1 helix: beta-3-ALA24, beta-3- LYS28, beta-3-LYS31, beta-2-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
- 5HG2
- Type
- protein
- Length
- 224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein G
- UniProt
- P19909
- Ligands
- MG, NH2
- Pockets
- 6 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Immunoglobulin G-binding protein G | protein | 56 | 30% helix, 43% strand | P19909 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D
- NH2 · Amino group · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.44 | 0.74 | 21 | empty |
| 2 | 113 | 0.39 | 0.76 | 16 | empty |
| 3 | 135 | 0.38 | 0.74 | 22 | empty |
| 4 | 60 | 0.34 | 0.77 | 12 | empty |
| 5 | 60 | 0.33 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 408 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 121 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 94 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (nonstandard).
Compared structures
- 5HG2 · Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28… · the same entry in another collection · chain D against D, 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 0.96
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 5HG2 · PDBe 5HG2 · UniProt P19909
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