MolNFT v1 · #14354 · protein
Structure of the oxa-1 class D beta-lactamase
1M6K · Beta-lactamase oxa-1: “Structure of the oxa-1 class D beta-lactamase”. X-ray diffraction, 4 pockets (best druggability 0.42). MolNFT v1 #14354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1M6K
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-1
- EC
- 3.5.2.6
- UniProt
- P13661
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase oxa-1 (EC 3.5.2.6) | protein | 250 | 39% helix, 21% strand | P13661 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.42 | 0.74 | 32 | MPD |
| 2 | 155 | 0.42 | 0.74 | 30 | MPD |
| 3 | 81 | 0.39 | 0.77 | 14 | MPD |
| 4 | 53 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 269 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
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 P13661
- Elsewhere: RCSB PDB 1M6K · PDBe 1M6K · UniProt P13661
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