Research workbench
Per-2 class a extended-spectrum beta-lactamase crystal structure in complex with avibactam at 2.4 ångström resolution
Analyse Per-2 class a extended-spectrum beta-lactamase crystal structure in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3G
- Type
- protein
- Length
- 1,114 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A2RP81
- Ligands
- NXL
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 279 | 43% helix, 21% strand | A2RP81 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 279 | 46% helix, 21% strand | A2RP81 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 281 | 44% helix, 21% strand | A2RP81 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 275 | 43% helix, 20% strand | A2RP81 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.69 | 0.95 | 18 | empty |
| 2 | 627 | 0.65 | 0.75 | 63 | PG4 |
| 3 | 378 | 0.59 | 0.76 | 36 | empty |
| 4 | 163 | 0.50 | 0.78 | 26 | empty |
| 5 | 156 | 0.43 | 0.75 | 32 | NXL |
Interfaces
4 interfaces between chains.
- B–D · 1037 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 388 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 299 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 111 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6D3G · PER-2 class A extended-spectrum beta-lactamase crystal structure in complex with… · 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 A2RP81
- Elsewhere: RCSB PDB 6D3G · PDBe 6D3G · UniProt A2RP81
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