MolNFT v1 · #165565 · protein
Adc-7 in complex with boronic acid transition state inhibitor PFC_001
6TZI · Beta-lactamase: “Adc-7 in complex with boronic acid transition state inhibitor PFC_001”. X-ray diffraction, 1 ligand (P1K), 13 pockets (best druggability 0.63). MolNFT v1 #165565 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6TZI
- 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
- P1K
- Pockets
- 13 · best druggability 0.63
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 | 41% helix, 20% strand | Q6DRA1 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 42% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 354 | 43% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- P1K · Phosphonooxy-[[4-[[2,2,2-tris(fluoranyl) ethylsulfonylamino]methyl]-1,2,3-triazol-1-yl]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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.63 | 0.76 | 54 | empty |
| 2 | 384 | 0.57 | 0.75 | 48 | empty |
| 3 | 398 | 0.57 | 0.74 | 53 | empty |
| 4 | 318 | 0.55 | 0.75 | 35 | P1K |
| 5 | 251 | 0.53 | 0.76 | 31 | P1K |
Interfaces
4 interfaces between chains.
- A–C · 527 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 453 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 251 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 201 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6TZI · ADC-7 in complex with boronic acid transition state inhibitor PFC_001 · the same entry in another collection · chain C against C, 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 6TZI · PDBe 6TZI · UniProt Q6DRA1
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