MolNFT v1 · #160742 · protein
Crystal structure of class D beta-lactamase oxa-48 with cefoxitin
6PT5 · Class D carbapenemase oxa-48: “Crystal structure of class D beta-lactamase oxa-48 with cefoxitin”. X-ray diffraction, 2 ligands (1S7, CL), 12 pockets (best druggability 0.73). MolNFT v1 #160742 on GenesisL1: 3D structure, binding…
- PDB
- 6PT5
- Type
- protein
- Length
- 979 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
- 1S7, CL
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 245 | 42% helix, 21% strand | A0A482LRD5 |
| B | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 247 | 42% helix, 20% strand | A0A482LRD5 |
| C | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 243 | 41% helix, 21% strand | A0A482LRD5 |
| D | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 244 | 38% helix, 20% strand | A0A482LRD5 |
Ligands and binding sites
- 1S7 · (2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl) amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.73 | 0.86 | 52 | CL |
| 2 | 719 | 0.72 | 0.79 | 80 | empty |
| 3 | 526 | 0.71 | 0.80 | 78 | CL, 1S7 |
| 4 | 251 | 0.62 | 0.81 | 42 | empty |
| 5 | 122 | 0.39 | 0.74 | 21 | 1S7 |
Interfaces
5 interfaces between chains.
- A–C · 970 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 965 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 102 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 52 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6PT5 · Crystal Structure of Class D Beta-lactamase OXA-48 with Cefoxitin · 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 6PT5 · PDBe 6PT5 · UniProt A0A482LRD5
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