MolNFT v1 · #65942 · protein
Crystal structure of oxa-48 beta-lactamase
3HBR: “Crystal structure of oxa-48 beta-lactamase”. X-ray diffraction, 7 pockets (best druggability 0.81). MolNFT v1 #65942 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HBR
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxa-48
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxa-48 (EC 3.5.2.6) | protein | 240 | 41% helix, 21% strand | Q6XEC0 |
| B | Oxa-48 (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | Q6XEC0 |
| C | Oxa-48 (EC 3.5.2.6) | protein | 240 | 42% helix, 20% strand | Q6XEC0 |
| D | Oxa-48 (EC 3.5.2.6) | protein | 239 | 42% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.81 | 0.85 | 107 | empty |
| 2 | 873 | 0.77 | 0.80 | 130 | empty |
| 3 | 157 | 0.55 | 0.81 | 22 | empty |
| 4 | 91 | 0.40 | 0.78 | 20 | empty |
| 5 | 156 | 0.40 | 0.73 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 998 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 966 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 101 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 3HBR · Crystal structure of OXA-48 beta-lactamase · 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 3HBR · PDBe 3HBR · UniProt Q6XEC0
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