MolNFT v1 · #138163 · protein
Adc-7 in complex with boronic acid transition state inhibitor CR167
5WAE · Beta-lactamase: “Adc-7 in complex with boronic acid transition state inhibitor CR167”. X-ray diffraction, 1 ligand (A1J), 11 pockets (best druggability 0.74). MolNFT v1 #138163 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5WAE
- Type
- protein
- Length
- 1,422 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
- A1J
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 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 | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 42% helix, 21% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 353 | 41% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- A1J · 3-(5,7,7-trihydroxy-2,2,7-trioxo-6-oxa-2lambda~6~-thia-3-aza-7lambda~5~-phospha-5-boraheptan-1-yl)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
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 | 1002 | 0.74 | 0.77 | 70 | empty |
| 2 | 771 | 0.67 | 0.75 | 83 | A1J |
| 3 | 218 | 0.52 | 0.77 | 41 | A1J |
| 4 | 210 | 0.50 | 0.76 | 31 | A1J |
| 5 | 211 | 0.50 | 0.76 | 35 | A1J |
Interfaces
5 interfaces between chains.
- B–C · 390 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 193 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 141 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 66 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5WAE · ADC-7 in complex with boronic acid transition state inhibitor CR167 · 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 5WAE · PDBe 5WAE · UniProt Q6DRA1
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