Research workbench
Crystal structure of L2 complexed with relebactam (16 hour soak)
Analyse Crystal structure of L2 complexed with relebactam (16 hour soak) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QW7
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9RBQ1
- Ligands
- DSN, MK7
- Pockets
- 10 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 270 | 47% helix, 18% strand | Q9RBQ1 |
Ligands and binding sites
- DSN · D-serine · ligand · chains A
- MK7 · (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy) amino]piperidine-2-carboxamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.41 | 0.82 | 15 | empty |
| 2 | 97 | 0.40 | 0.77 | 19 | empty |
| 3 | 112 | 0.39 | 0.75 | 14 | empty |
| 4 | 98 | 0.38 | 0.76 | 18 | empty |
| 5 | 56 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QW7 · Crystal structure of L2 complexed with relebactam (16 hour soak) · 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 Q9RBQ1
- Elsewhere: RCSB PDB 6QW7 · PDBe 6QW7 · UniProt Q9RBQ1
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