MolNFT v1 · #168440 · protein
The crystal structure of a beta-lactamase from staphylococcus aureus subsp. aureus USA300_TCH1516
6WGR: “The crystal structure of a beta-lactamase from staphylococcus aureus subsp. aureus USA300_TCH1516”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #168440 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WGR
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- D2J684
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 43% helix, 18% strand | D2J684 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.76 | 0.82 | 53 | empty |
| 2 | 889 | 0.75 | 0.78 | 70 | empty |
| 3 | 832 | 0.73 | 0.77 | 49 | empty |
| 4 | 104 | 0.38 | 0.76 | 17 | EPE |
| 5 | 92 | 0.37 | 0.76 | 16 | EPE |
Interfaces
2 interfaces between chains.
- A–B · 432 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6WGR · The crystal structure of a beta-lactamase from Staphylococcus aureus subsp. aureus… · 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 D2J684
- Elsewhere: RCSB PDB 6WGR · PDBe 6WGR · UniProt D2J684
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