Research workbench
Crystal structure of the N-terminal fic domain of BEP8 protein (virb- translocated bartonella effector protein) from bartonella sp. 1-1C
Analyse Crystal structure of the N-terminal fic domain of BEP8 protein (virb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PY3
- Type
- protein
- Length
- 2,142 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bartonella effector protein (bep) substrate of virb T4SS
- UniProt
- E6YV77
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, I | Bartonella effector protein (bep) substrate of virb T4SS | protein | 213 | 57% helix, 4% strand | E6YV77 |
| C, D, H | Bartonella effector protein (bep) substrate of virb T4SS | protein | 216 | 56% helix, 4% strand | E6YV77 |
| E | Bartonella effector protein (bep) substrate of virb T4SS | protein | 215 | 55% helix, 4% strand | E6YV77 |
| F | Bartonella effector protein (bep) substrate of virb T4SS | protein | 211 | 55% helix, 4% strand | E6YV77 |
| G | Bartonella effector protein (bep) substrate of virb T4SS | protein | 217 | 54% helix, 4% strand | E6YV77 |
| J | Bartonella effector protein (bep) substrate of virb T4SS | protein | 212 | 56% helix, 4% strand | E6YV77 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains I, J
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 | 1053 | 0.82 | 0.83 | 134 | EDO |
| 2 | 782 | 0.72 | 0.78 | 66 | empty |
| 3 | 280 | 0.71 | 0.85 | 44 | empty |
| 4 | 253 | 0.70 | 0.85 | 47 | empty |
| 5 | 610 | 0.68 | 0.77 | 61 | empty |
Interfaces
15 interfaces between chains.
- C–G · 997 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 989 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 986 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 477 Ų buried · 8 hydrogen bonds · protein-protein
- B–I · 408 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4PY3 · Crystal Structure of the N-terminal FIC domain of Bep8 protein (VirB-translocated… · 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 E6YV77
- Elsewhere: RCSB PDB 4PY3 · PDBe 4PY3 · UniProt E6YV77
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