MolNFT v1 · #63342 · protein
Xre-family like protein from pseudomonas syringae pv. tomato str. DC3000
3F6W: “Xre-family like protein from pseudomonas syringae pv. tomato str. DC3000”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #63342 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3F6W
- Type
- protein
- Length
- 408 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xre-family like protein
- UniProt
- Q889N2
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Xre-family like protein | protein | 82 | 73% helix, 0% strand | Q889N2 |
| B, C | Xre-family like protein | protein | 82 | 74% helix, 0% strand | Q889N2 |
| E | Xre-family like protein | protein | 80 | 71% helix, 0% strand | Q889N2 |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.62 | 0.78 | 44 | BTB |
| 2 | 117 | 0.41 | 0.75 | 15 | empty |
| 3 | 77 | 0.37 | 0.77 | 16 | empty |
| 4 | 53 | 0.30 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1220 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1160 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 677 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 357 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 83 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3F6W · XRE-family like protein from Pseudomonas syringae pv. tomato str. DC3000 · 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 Q889N2
- Elsewhere: RCSB PDB 3F6W · PDBe 3F6W · UniProt Q889N2
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