Research workbench
Adc-7 in complex with boronic acid transition state inhibitor S17079
Analyse Adc-7 in complex with boronic acid transition state inhibitor S17079 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TZF
- 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
- KAS
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 42% helix, 19% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 354 | 41% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- KAS · 3-(1-{[hydroxy(phosphonooxy)boranyl]methyl}-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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.62 | 0.77 | 56 | empty |
| 2 | 319 | 0.56 | 0.76 | 40 | KAS |
| 3 | 303 | 0.55 | 0.75 | 33 | empty |
| 4 | 245 | 0.54 | 0.77 | 39 | KAS |
| 5 | 225 | 0.53 | 0.77 | 41 | KAS |
Interfaces
4 interfaces between chains.
- B–C · 446 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 427 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 154 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6TZF · ADC-7 in complex with boronic acid transition state inhibitor S17079 · 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 6TZF · PDBe 6TZF · UniProt Q6DRA1
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