Research workbench
Structure of adc-7 beta-lactamase in complex with boronic acid inhibitor S02030
Analyse Structure of adc-7 beta-lactamase in complex with boronic acid inhibitor S02030 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U0X
- Type
- protein
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adc-7 beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6DRA1
- Ligands
- ZXM, PO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| A | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 355 | 43% helix, 20% strand | Q6DRA1 |
| C | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 356 | 41% helix, 20% strand | Q6DRA1 |
| D | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 352 | 41% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- ZXM · 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl) amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid · ligand · 4 copies · chains B, A, C, D
- PO4 · Phosphate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.73 | 0.79 | 61 | empty |
| 2 | 451 | 0.60 | 0.75 | 50 | empty |
| 3 | 279 | 0.56 | 0.77 | 45 | ZXM |
| 4 | 191 | 0.55 | 0.80 | 30 | ZXM |
| 5 | 251 | 0.55 | 0.77 | 39 | ZXM |
Interfaces
4 interfaces between chains.
- B–C · 377 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 181 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4U0X · Structure of ADC-7 beta-lactamase in complex with boronic acid inhibitor S02030 · the same entry in another collection · chain B against B, 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 Q6DRA1
- Elsewhere: RCSB PDB 4U0X · PDBe 4U0X · UniProt Q6DRA1
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