Research workbench
Crystal structure of blac from mycobacterium tuberculosis bound to phosphate
Analyse Crystal structure of blac from mycobacterium tuberculosis bound to phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NJ2
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A0T9EA39
- Ligands
- ETE, AE4, PO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 272 | 45% helix, 17% strand | A0A0T9EA39 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 46% helix, 17% strand | A0A0T9EA39 |
Ligands and binding sites
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · chains B
- AE4 · 3,6,9,12,15-pentaoxaheptadecan-1-ol · ligand · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.51 | 0.73 | 36 | empty |
| 2 | 150 | 0.47 | 0.77 | 17 | empty |
| 3 | 101 | 0.38 | 0.75 | 20 | PO4 |
| 4 | 87 | 0.36 | 0.76 | 20 | PO4, ACT |
| 5 | 67 | 0.35 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 260 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5NJ2 · Crystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate · 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 A0A0T9EA39
- Elsewhere: RCSB PDB 5NJ2 · PDBe 5NJ2 · UniProt A0A0T9EA39
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