MolNFT v1 · #176432 · protein
Oxa-48 carbapenemase in complex with (R)-2-(1-hydroxy-1,3- DIHYDROBENZO[C][1,2]OXABOROL-3-YL)ACRYLIC acid
7DML · Beta-lactamase: “Oxa-48 carbapenemase in complex with (R)-2-(1-hydroxy-1,3- DIHYDROBENZO[C][1,2]OXABOROL-3-YL)ACRYLIC acid”. X-ray diffraction, 1 ligand (H9O), 6 pockets (best druggability 0.81). MolNFT v1 #176432 on GenesisL1: 3D…
- PDB
- 7DML
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- H9O
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- H9O · 2-[(3R)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid · ligand · 4 copies · chains A, B, C, 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 | 828 | 0.81 | 0.84 | 109 | H9O |
| 2 | 375 | 0.61 | 0.77 | 40 | empty |
| 3 | 174 | 0.54 | 0.79 | 22 | empty |
| 4 | 121 | 0.39 | 0.75 | 18 | H9O |
| 5 | 57 | 0.36 | 0.79 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 587 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 343 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 188 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 166 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, carboxylation).
Compared structures
- 7DML · OXA-48 carbapenemase in complex with (R)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-y… · 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 7DML · PDBe 7DML · UniProt Q6XEC0
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