Research workbench
Class D beta-lactamase in complex with beta-lactam antibiotic
Analyse Class D beta-lactamase in complex with beta-lactam antibiotic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PXX
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- 5R7, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 40% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- 5R7 · (2~{S},3~{R})-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.79 | 0.81 | 127 | 5R7, EDO, CL |
| 2 | 58 | 0.39 | 0.80 | 20 | empty |
| 3 | 60 | 0.38 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6PXX · Class D beta-lactamase in complex with beta-lactam antibiotic · 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 Q6XEC0
- Elsewhere: RCSB PDB 6PXX · PDBe 6PXX · UniProt Q6XEC0
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