MolNFT v1 · #137844 · protein
Adc-7 in complex with boronic acid transition state inhibitor SM23
5W13 · Beta-lactamase: “Adc-7 in complex with boronic acid transition state inhibitor SM23”. X-ray diffraction, 1 ligand (SM2), 14 pockets (best druggability 0.69). MolNFT v1 #137844 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5W13
- Type
- protein
- Length
- 1,426 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
- SM2
- Pockets
- 14 · best druggability 0.69
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 | 354 | 42% helix, 19% strand | Q6DRA1 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 42% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 41% helix, 20% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- SM2 · (1R)-1-(2-thienylacetylamino)-1-(3-carboxyphenyl) methylboronic 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.69 | 0.76 | 91 | SM2 |
| 2 | 506 | 0.65 | 0.77 | 63 | empty |
| 3 | 433 | 0.58 | 0.74 | 55 | empty |
| 4 | 266 | 0.56 | 0.77 | 43 | SM2 |
| 5 | 255 | 0.56 | 0.78 | 40 | SM2 |
Interfaces
4 interfaces between chains.
- A–C · 524 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 440 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 331 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 233 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5W13 · ADC-7 in complex with boronic acid transition state inhibitor SM23 · the same entry in another collection · chain D against D, 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 5W13 · PDBe 5W13 · UniProt Q6DRA1
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