Research workbench
H/L (SLPH/SLPL) complex from C. difficile (R7404 strain)
Analyse H/L (SLPH/SLPL) complex from C. difficile (R7404 strain) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ACX
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-layer protein
- EC
- 3.5.1.28
- UniProt
- Q8KHI4, Q9AEM2
- Ligands
- NAG, SO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-layer protein | protein | 313 | 26% helix, 33% strand | Q8KHI4 |
| B | S-layer protein (EC 3.5.1.28) | protein | 369 | 40% helix, 18% strand | Q9AEM2 |
| C | S-layer protein | protein | 278 | 28% helix, 30% strand | Q8KHI4 |
| D | S-layer protein (EC 3.5.1.28) | protein | 373 | 38% helix, 18% strand | Q9AEM2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.71 | 0.75 | 101 | empty |
| 2 | 406 | 0.59 | 0.75 | 47 | NAG, SO4 |
| 3 | 144 | 0.57 | 0.82 | 26 | empty |
| 4 | 172 | 0.56 | 0.81 | 27 | empty |
| 5 | 344 | 0.56 | 0.75 | 34 | NAG, SO4 |
Interfaces
5 interfaces between chains.
- C–D · 2463 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2400 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 573 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 543 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7ACX · H/L (SLPH/SLPL) complex from C. difficile (R7404 strain) · 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 Q8KHI4
- Every structure of UniProt Q9AEM2
- Elsewhere: RCSB PDB 7ACX · PDBe 7ACX · UniProt Q8KHI4 · UniProt Q9AEM2
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