Research workbench
Crystal structure of shaft pilin spaa from lactobacillus rhamnosus gg - D295N mutant
Analyse Crystal structure of shaft pilin spaa from lactobacillus rhamnosus gg - D295N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HTS
- Type
- protein
- Length
- 1,522 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface protein spaa
- UniProt
- C7T9P4
- Pockets
- 14 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell surface protein spaa | protein | 259 | 6% helix, 45% strand | C7T9P4 |
| B | Cell surface protein spaa | protein | 264 | 6% helix, 44% strand | C7T9P4 |
| C | Cell surface protein spaa | protein | 254 | 6% helix, 46% strand | C7T9P4 |
| D | Cell surface protein spaa | protein | 260 | 6% helix, 45% strand | C7T9P4 |
| E | Cell surface protein spaa | protein | 245 | 7% helix, 47% strand | C7T9P4 |
| F | Cell surface protein spaa | protein | 240 | 7% helix, 46% strand | C7T9P4 |
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.62 | 0.80 | 33 | empty |
| 2 | 341 | 0.61 | 0.78 | 37 | empty |
| 3 | 499 | 0.60 | 0.74 | 52 | empty |
| 4 | 162 | 0.51 | 0.78 | 28 | empty |
| 5 | 94 | 0.42 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–E · 617 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 413 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 251 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 isopeptide (isopeptide).
Compared structures
- 5HTS · Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - D295N mutant · the same entry in another collection · chain A against A, 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 C7T9P4
- Elsewhere: RCSB PDB 5HTS · PDBe 5HTS · UniProt C7T9P4
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