Research workbench
Adc-7 in complex with boronic acid transition state inhibitor EC04
Analyse Adc-7 in complex with boronic acid transition state inhibitor EC04 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W12
- Type
- protein
- Length
- 1,423 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
- 9TG
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 353 | 40% helix, 20% strand | Q6DRA1 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 42% helix, 19% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 41% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- 9TG · 3-[(2R)-2-borono-2-{[(thiophen-2-yl) acetyl]amino}ethyl]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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.74 | 0.77 | 71 | empty |
| 2 | 704 | 0.68 | 0.76 | 79 | 9TG |
| 3 | 237 | 0.56 | 0.78 | 44 | 9TG |
| 4 | 263 | 0.55 | 0.77 | 36 | 9TG |
| 5 | 234 | 0.54 | 0.77 | 34 | 9TG |
Interfaces
5 interfaces between chains.
- B–C · 405 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 176 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5W12 · ADC-7 in complex with boronic acid transition state inhibitor EC04 · 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 5W12 · PDBe 5W12 · UniProt Q6DRA1
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