Research workbench
Adc-7 in complex with boronic acid transition state inhibitor CR157
Analyse Adc-7 in complex with boronic acid transition state inhibitor CR157 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WAC
- Type
- protein
- Length
- 1,418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6DRA1
- Ligands
- A1M
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 42% helix, 20% strand | Q6DRA1 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 42% helix, 19% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 352 | 40% helix, 20% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 352 | 41% helix, 19% strand | Q6DRA1 |
Ligands and binding sites
- A1M · Phosphonooxy-[[[4-(1~{H}-1,2,3,4-tetrazol-5-yl) phenyl]sulfonylamino]methyl]borinic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.66 | 0.76 | 78 | A1M |
| 2 | 318 | 0.58 | 0.77 | 45 | empty |
| 3 | 249 | 0.56 | 0.78 | 41 | A1M |
| 4 | 248 | 0.54 | 0.77 | 38 | A1M |
| 5 | 197 | 0.50 | 0.77 | 35 | A1M |
Interfaces
4 interfaces between chains.
- A–C · 503 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 439 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 264 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 182 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5WAC · ADC-7 in complex with boronic acid transition state inhibitor CR157 · 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 Q6DRA1
- Elsewhere: RCSB PDB 5WAC · PDBe 5WAC · UniProt Q6DRA1
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