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The 1.4 a structure of the class D beta-lactamase oxa-1 K70D complexed with oxacillin
Analyse The 1.4 a structure of the class D beta-lactamase oxa-1 K70D complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MLL
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-1
- EC
- 3.5.2.6
- UniProt
- P13661
- Ligands
- 1S6, PO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-lactamase oxa-1 (EC 3.5.2.6) | protein | 250 | 40% helix, 21% strand | P13661 |
| B, C | Beta-lactamase oxa-1 (EC 3.5.2.6) | protein | 251 | 39% helix, 21% strand | P13661 |
Ligands and binding sites
- 1S6 · (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.76 | 0.78 | 115 | 1S6, PO4 |
| 2 | 425 | 0.69 | 0.81 | 50 | 1S6 |
| 3 | 381 | 0.59 | 0.76 | 34 | PO4 |
| 4 | 119 | 0.38 | 0.74 | 25 | 1S6 |
| 5 | 105 | 0.37 | 0.74 | 22 | 1S6 |
Interfaces
5 interfaces between chains.
- C–D · 686 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 608 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4MLL · The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin · the same entry in another collection · chain D against D, TM-score 1.00
- P13661 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-1 (P13661) · a predicted model of the same protein · chain C 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 P13661
- Elsewhere: RCSB PDB 4MLL · PDBe 4MLL · UniProt P13661
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