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Periplasmic domain of the T3SS inner membrane protein prgh from S.TYPHIMURIUM (fragment 170-392)
Analyse Periplasmic domain of the T3SS inner membrane protein prgh from S.TYPHIMURIUM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GR1
- Type
- protein
- Length
- 1,532 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein prgh
- UniProt
- P41783
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein prgh | protein | 195 | 41% helix, 23% strand | P41783 |
| B, D | Protein prgh | protein | 193 | 41% helix, 22% strand | P41783 |
| C | Protein prgh | protein | 190 | 42% helix, 23% strand | P41783 |
| E | Protein prgh | protein | 192 | 40% helix, 23% strand | P41783 |
| F, G | Protein prgh | protein | 189 | 41% helix, 22% strand | P41783 |
| H | Protein prgh | protein | 191 | 46% helix, 22% strand | P41783 |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.79 | 0.81 | 103 | empty |
| 2 | 1101 | 0.77 | 0.79 | 85 | empty |
| 3 | 806 | 0.71 | 0.77 | 71 | empty |
| 4 | 315 | 0.65 | 0.81 | 37 | empty |
| 5 | 245 | 0.61 | 0.81 | 29 | empty |
Interfaces
14 interfaces between chains.
- E–G · 1036 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 960 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 957 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 1 hydrogen bond · protein-protein
- D–H · 574 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3GR1 · Periplasmic domain of the T3SS inner membrane protein PrgH from S.typhimurium (fragment… · the same entry in another collection · chain H against H, TM-score 1.00
- P41783 · AlphaFold monomer V2.0 prediction for protein prgh (P41783) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P41783
- Elsewhere: RCSB PDB 3GR1 · PDBe 3GR1 · UniProt P41783
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