MolNFT v1 · #90027 · protein
Clbp in complex boron-based inhibitor
4E6X · Clbp peptidase: “Clbp in complex boron-based inhibitor”. X-ray diffraction, 2 ligands (0NG, PO4), 6 pockets (best druggability 0.59). MolNFT v1 #90027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4E6X
- Type
- protein
- Length
- 916 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
- 0NG, PO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clbp peptidase (EC 3.5.2.6) | protein | 310 | 35% helix, 23% strand | Q8FGC8 |
| B | Clbp peptidase (EC 3.5.2.6) | protein | 301 | 37% helix, 23% strand | Q8FGC8 |
| C | Clbp peptidase (EC 3.5.2.6) | protein | 305 | 35% helix, 24% strand | Q8FGC8 |
Ligands and binding sites
- 0NG · ({[(chloromethyl)sulfonyl]amino}methyl)boronic acid · ligand · 2 copies · chains B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.59 | 0.74 | 55 | empty |
| 2 | 359 | 0.56 | 0.75 | 42 | empty |
| 3 | 385 | 0.55 | 0.73 | 38 | empty |
| 4 | 158 | 0.42 | 0.74 | 33 | PO4 |
| 5 | 151 | 0.41 | 0.74 | 25 | 0NG |
Interfaces
3 interfaces between chains.
- A–B · 96 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4E6X · ClbP in complex boron-based inhibitor · 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 4E6X · PDBe 4E6X · UniProt Q8FGC8
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