Research workbench
Crystal structure of the bid domain of bepe from bartonella henselae
Analyse Crystal structure of the bid domain of bepe from bartonella henselae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YK3
- Type
- protein
- Length
- 434 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bepe protein
- UniProt
- Q5QT01
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bepe protein | protein | 120 | 76% helix, 3% strand | Q5QT01 |
| B | Bepe protein | protein | 107 | 71% helix, 4% strand | Q5QT01 |
| C | Bepe protein | protein | 107 | 75% helix, 4% strand | Q5QT01 |
| D | Bepe protein | protein | 100 | 72% helix, 4% strand | Q5QT01 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.56 | 0.76 | 36 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 385 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YK3 · Crystal Structure of the BID Domain of BepE from Bartonella henselae · 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 Q5QT01
- Elsewhere: RCSB PDB 4YK3 · PDBe 4YK3 · UniProt Q5QT01
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