Research workbench
Invg secretin domain beta-barrel from salmonella spi-1 injectisome nc- base
Analyse Invg secretin domain beta-barrel from salmonella spi-1 injectisome nc- base in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PEE
- Type
- protein
- Length
- 5,175 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein invg
- UniProt
- P35672
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 14% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H, I, J, K, L, M, N, O, P | Protein invg | protein | 345 | 14% helix, 49% strand | P35672 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · 45 copies · chains A, P, B, C, D, F, G, H, I, J, K, L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.86 | 0.92 | 102 | empty |
| 2 | 541 | 0.86 | 0.91 | 103 | empty |
| 3 | 415 | 0.83 | 0.91 | 78 | empty |
| 4 | 352 | 0.82 | 0.91 | 63 | empty |
| 5 | 231 | 0.77 | 0.91 | 42 | empty |
Interfaces
30 interfaces between chains.
- I–J · 5151 Ų buried · 62 hydrogen bonds · protein-protein
- H–I · 5090 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 5070 Ų buried · 54 hydrogen bonds · protein-protein
- K–L · 5069 Ų buried · 54 hydrogen bonds · protein-protein
- F–G · 5062 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 6PEE · InvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base · the same entry in another collection · chain P against P, 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 P35672
- Elsewhere: RCSB PDB 6PEE · PDBe 6PEE · UniProt P35672
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