MolNFT v1 · #138165 · protein
Adc-7 in complex with boronic acid transition state inhibitor S06017
5WAG · Beta-lactamase: “Adc-7 in complex with boronic acid transition state inhibitor S06017”. X-ray diffraction, 1 ligand (A0V), 11 pockets (best druggability 0.71). MolNFT v1 #138165 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5WAG
- 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
- A0V
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| A | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 41% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 42% helix, 19% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 43% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- A0V · 1-{[hydroxy(phosphonooxy)boranyl]methyl}-1H-1,2,3-triazole-4-carboxylic acid · ligand · 4 copies · chains B, A, C, D
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.71 | 0.76 | 87 | A0V, SIN |
| 2 | 437 | 0.63 | 0.77 | 53 | empty |
| 3 | 416 | 0.57 | 0.74 | 54 | empty |
| 4 | 259 | 0.56 | 0.78 | 43 | A0V |
| 5 | 236 | 0.53 | 0.77 | 41 | A0V |
Interfaces
4 interfaces between chains.
- A–C · 601 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 442 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 311 Ų buried · 1 hydrogen bond · protein-protein
- B–A · 213 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5WAG · ADC-7 in complex with boronic acid transition state inhibitor S06017 · the same entry in another collection · chain B against B, 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 5WAG · PDBe 5WAG · UniProt Q6DRA1
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