Research workbench
Crystal structure of ges-5 beta-lactamase in complex with boronic inhibitor cpd 3
Analyse Crystal structure of ges-5 beta-lactamase in complex with boronic inhibitor cpd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q35
- Type
- protein
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q09HD0
- Ligands
- HD5
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 267 | 49% helix, 19% strand | Q09HD0 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 268 | 48% helix, 19% strand | Q09HD0 |
Ligands and binding sites
- HD5 · [5-(aminomethyl)-1-benzothiophen-2-yl]boronic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.71 | 0.80 | 50 | EDO, DMS |
| 2 | 112 | 0.49 | 0.80 | 16 | empty |
| 3 | 101 | 0.44 | 0.78 | 16 | EDO |
| 4 | 63 | 0.36 | 0.78 | 19 | DMS |
| 5 | 66 | 0.35 | 0.77 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 disulfide (covalent ligand, disulfide, additive adduct).
Compared structures
- 6Q35 · Crystal structure of GES-5 beta-lactamase in complex with boronic inhibitor cpd 3 · 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 Q09HD0
- Elsewhere: RCSB PDB 6Q35 · PDBe 6Q35 · UniProt Q09HD0
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