MolNFT v1 · #27483 · protein
Complex structure of Y.PESTIS virulence factors yopn and tyea
1XL3 · Secretion control protein: “Complex structure of Y.PESTIS virulence factors yopn and tyea”. X-ray diffraction, 9 pockets (best druggability 0.67). MolNFT v1 #27483 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XL3
- Type
- protein
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secretion control protein; Protein type a
- UniProt
- P16161
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secretion control protein | protein | 202 | 75% helix, 0% strand | — |
| B | Secretion control protein | protein | 206 | 81% helix, 0% strand | — |
| C | Protein type a | protein | 91 | 75% helix, 0% strand | P16161 |
| D | Protein type a | protein | 85 | 76% helix, 0% strand | P16161 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.67 | 0.87 | 21 | empty |
| 2 | 357 | 0.62 | 0.78 | 49 | empty |
| 3 | 196 | 0.55 | 0.79 | 43 | empty |
| 4 | 160 | 0.48 | 0.77 | 33 | empty |
| 5 | 132 | 0.44 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1120 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1080 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 528 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 396 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (methylation).
Compared structures
- 1XL3 · Complex structure of Y.pestis virulence Factors YopN and TyeA · 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 P16161
- Elsewhere: RCSB PDB 1XL3 · PDBe 1XL3 · UniProt P16161
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