Research workbench
Crystal structure of class D beta-lactamase oxa-48 with meropenem
Analyse Crystal structure of class D beta-lactamase oxa-48 with meropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PT1
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class D carbapenemase oxa-48
- EC
- 3.5.2.6
- UniProt
- A0A482LRD5
- Ligands
- MER, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 247 | 40% helix, 20% strand | A0A482LRD5 |
| B, D | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 244 | 40% helix, 21% strand | A0A482LRD5 |
Ligands and binding sites
- MER · (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.81 | 0.84 | 116 | CL |
| 2 | 585 | 0.79 | 0.85 | 87 | CL |
| 3 | 102 | 0.43 | 0.78 | 21 | MER |
| 4 | 125 | 0.41 | 0.75 | 21 | CL, MER |
| 5 | 85 | 0.39 | 0.77 | 18 | MER |
Interfaces
5 interfaces between chains.
- A–B · 981 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 975 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 127 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6PT1 · Crystal Structure of Class D Beta-lactamase OXA-48 with Meropenem · 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 A0A482LRD5
- Elsewhere: RCSB PDB 6PT1 · PDBe 6PT1 · UniProt A0A482LRD5
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