Research workbench
Crystal structure of bacb, an enzyme involved in bacilysin synthesis, in tetragonal form
Analyse Crystal structure of bacb, an enzyme involved in bacilysin synthesis, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H7Y
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacilysin biosynthesis protein bacb
- UniProt
- P39639
- Ligands
- PPY, CO, FE
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacilysin biosynthesis protein bacb | protein | 220 | 2% helix, 59% strand | P39639 |
| B | Bacilysin biosynthesis protein bacb | protein | 222 | 4% helix, 56% strand | P39639 |
Ligands and binding sites
- PPY · 3-phenylpyruvic acid · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- FE · Fe (III) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.83 | 0.84 | 92 | empty |
| 2 | 67 | 0.72 | 0.97 | 21 | PPY |
| 3 | 59 | 0.69 | 0.97 | 20 | PPY |
| 4 | 77 | 0.34 | 0.75 | 19 | empty |
| 5 | 53 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3H7Y · Crystal structure of BacB, an enzyme involved in Bacilysin synthesis, in tetragonal form · the same entry in another collection · chain A against A, TM-score 1.00
- P39639 · AlphaFold monomer V2.0 prediction for H2HPP isomerase (P39639) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P39639
- Elsewhere: RCSB PDB 3H7Y · PDBe 3H7Y · UniProt P39639
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