MolNFT v1 · #109962 · protein
Crystal structure of the fic domain of BEP5 protein (virb-translocated bartonella effector protein) from bartonella clarridgeiae
4XI8 · Bartonella effector protein (bep) substrate of virb T4SS: “Crystal structure of the fic domain of BEP5 protein (virb-translocated bartonella effector protein) from…”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 4XI8
- Type
- protein
- Length
- 1,197 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bartonella effector protein (bep) substrate of virb T4SS
- UniProt
- E6YGF5
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bartonella effector protein (bep) substrate of virb T4SS | protein | 211 | 56% helix, 2% strand | E6YGF5 |
| B | Bartonella effector protein (bep) substrate of virb T4SS | protein | 208 | 56% helix, 2% strand | E6YGF5 |
| C | Bartonella effector protein (bep) substrate of virb T4SS | protein | 203 | 55% helix, 2% strand | E6YGF5 |
| D | Bartonella effector protein (bep) substrate of virb T4SS | protein | 206 | 57% helix, 2% strand | E6YGF5 |
| E | Bartonella effector protein (bep) substrate of virb T4SS | protein | 208 | 56% helix, 2% strand | E6YGF5 |
| F | Bartonella effector protein (bep) substrate of virb T4SS | protein | 161 | 59% helix, 0% strand | E6YGF5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.72 | 0.77 | 68 | empty |
| 2 | 887 | 0.71 | 0.76 | 96 | empty |
| 3 | 72 | 0.71 | 0.95 | 17 | empty |
| 4 | 467 | 0.64 | 0.76 | 55 | empty |
| 5 | 278 | 0.58 | 0.77 | 41 | empty |
Interfaces
8 interfaces between chains.
- B–C · 760 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 747 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 619 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 590 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XI8 · Crystal Structure of the FIC domain of Bep5 protein (VirB-translocated Bartonella… · 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 E6YGF5
- Elsewhere: RCSB PDB 4XI8 · PDBe 4XI8 · UniProt E6YGF5
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