MolNFT v1 · #151028 · protein
Crystal structure of oxa-517 beta-lactamase
6HB8: “Crystal structure of oxa-517 beta-lactamase”. X-ray diffraction, 3 ligands (ETX, SO4, CL), 7 pockets (best druggability 0.78). MolNFT v1 #151028 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HB8
- Type
- protein
- Length
- 972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A1U8YI81
- Ligands
- ETX, SO4, CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 40% helix, 21% strand | A0A1U8YI81 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | A0A1U8YI81 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | A0A1U8YI81 |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · chains A, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.78 | 0.81 | 100 | GOL, SO4, CL |
| 2 | 78 | 0.70 | 0.95 | 19 | CL, SO4 |
| 3 | 356 | 0.64 | 0.79 | 54 | SO4, GOL |
| 4 | 307 | 0.62 | 0.79 | 47 | SO4 |
| 5 | 216 | 0.60 | 0.81 | 35 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 968 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 962 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 278 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 108 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6HB8 · Crystal structure of OXA-517 beta-lactamase · 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 A0A1U8YI81
- Elsewhere: RCSB PDB 6HB8 · PDBe 6HB8 · UniProt A0A1U8YI81
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