MolNFT v1 · #165566 · protein
Adc-7 in complex with boronic acid transition state inhibitor ME_096
6TZJ · Beta-lactamase: “Adc-7 in complex with boronic acid transition state inhibitor ME_096”. X-ray diffraction, 2 ligands (PKV, GLY), 10 pockets (best druggability 0.72). MolNFT v1 #165566 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6TZJ
- Type
- protein
- Length
- 1,425 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
- PKV, GLY
- Pockets
- 10 · best druggability 0.72
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 | 355 | 42% helix, 20% strand | Q6DRA1 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 42% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- PKV · [4-[[(4-methylphenyl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]methyl-phosphonooxy-borinic acid · ligand · 4 copies · chains A, B, C, D
- GLY · Glycine · ligand · 3 copies · chains A, 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 | 971 | 0.72 | 0.76 | 78 | empty |
| 2 | 738 | 0.68 | 0.75 | 70 | PKV |
| 3 | 289 | 0.58 | 0.78 | 37 | empty |
| 4 | 239 | 0.54 | 0.77 | 39 | PKV, GLY |
| 5 | 212 | 0.52 | 0.77 | 38 | PKV, GLY |
Interfaces
5 interfaces between chains.
- B–C · 349 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 204 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6TZJ · ADC-7 in complex with boronic acid transition state inhibitor ME_096 · 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 6TZJ · PDBe 6TZJ · UniProt Q6DRA1
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