Research workbench
Oxa-48 carbapanemase, meropenem complex
Analyse Oxa-48 carbapanemase, meropenem complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P98
- Type
- protein
- Length
- 487 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
- KE1, CA, CD, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 245 | 40% helix, 20% strand | Q6XEC0 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- KE1 · meropenem, bound form · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, 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 | 873 | 0.77 | 0.81 | 121 | KE1, CL |
| 2 | 56 | 0.39 | 0.81 | 17 | empty |
| 3 | 57 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6P98 · OXA-48 carbapanemase, meropenem complex · 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 6P98 · PDBe 6P98 · UniProt Q6XEC0
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