Research workbench
Clbp in complex with 3-aminophenyl boronic acid
Analyse Clbp in complex with 3-aminophenyl boronic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E6W
- Type
- protein
- Length
- 991 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clbp peptidase
- EC
- 3.5.2.6
- UniProt
- Q8FGC8
- Ligands
- APB, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clbp peptidase (EC 3.5.2.6) | protein | 329 | 37% helix, 21% strand | Q8FGC8 |
| B | Clbp peptidase (EC 3.5.2.6) | protein | 332 | 37% helix, 21% strand | Q8FGC8 |
| C | Clbp peptidase (EC 3.5.2.6) | protein | 330 | 37% helix, 21% strand | Q8FGC8 |
Ligands and binding sites
- APB · M-aminophenylboronic acid · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.76 | 0.80 | 72 | empty |
| 2 | 308 | 0.57 | 0.77 | 56 | APB, PO4 |
| 3 | 255 | 0.55 | 0.77 | 48 | APB, PO4 |
| 4 | 132 | 0.44 | 0.77 | 23 | empty |
| 5 | 169 | 0.44 | 0.74 | 36 | APB, PO4 |
Interfaces
2 interfaces between chains.
- A–B · 1292 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 4E6W · ClbP in complex with 3-aminophenyl boronic acid · 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 Q8FGC8
- Elsewhere: RCSB PDB 4E6W · PDBe 4E6W · UniProt Q8FGC8
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