Research workbench
Adc-7 in complex with boronic acid transition state inhibitor S03043
Analyse Adc-7 in complex with boronic acid transition state inhibitor S03043 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W14
- Type
- protein
- Length
- 1,424 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
- 9TJ
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 43% helix, 20% strand | Q6DRA1 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 42% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 43% helix, 19% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 352 | 40% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- 9TJ · 3-{1-[(2R)-2-borono-2-{[(thiophen-2-yl) acetyl]amino}ethyl]-1H-1,2,3-triazol-4-yl}benzoic 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.74 | 0.77 | 72 | empty |
| 2 | 391 | 0.59 | 0.76 | 60 | 9TJ |
| 3 | 340 | 0.58 | 0.76 | 41 | 9TJ |
| 4 | 392 | 0.57 | 0.75 | 49 | empty |
| 5 | 253 | 0.55 | 0.77 | 45 | 9TJ |
Interfaces
5 interfaces between chains.
- B–C · 395 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 175 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 118 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 69 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5W14 · ADC-7 in complex with boronic acid transition state inhibitor S03043 · 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 5W14 · PDBe 5W14 · UniProt Q6DRA1
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