Research workbench
Crystal structure of tem-1 beta-lactamase in complex with boron-based inhibitor EC25
Analyse Crystal structure of tem-1 beta-lactamase in complex with boron-based inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OQG
- Type
- protein
- Length
- 1,578 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ampicillin resistance protein
- EC
- 3.5.2.6
- UniProt
- Q79DR3
- Ligands
- 2UL, ZN
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ampicillin resistance protein (EC 3.5.2.6) | protein | 263 | 44% helix, 17% strand | Q79DR3 |
Ligands and binding sites
- 2UL · 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid · ligand · 5 copies · chains A, B, C, D, F
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.75 | 0.80 | 83 | 2UL |
| 2 | 256 | 0.48 | 0.73 | 32 | empty |
| 3 | 126 | 0.43 | 0.77 | 21 | 2UL |
| 4 | 160 | 0.42 | 0.74 | 25 | empty |
| 5 | 104 | 0.42 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–D · 459 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 300 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 115 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 4OQG · Crystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25 · 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 Q79DR3
- Elsewhere: RCSB PDB 4OQG · PDBe 4OQG · UniProt Q79DR3
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