MolNFT v1 · #120421 · protein
Crystal structure of ampc ber adenylylated by acetyl-AMP
5GZW · Beta-lactamase: “Crystal structure of ampc ber adenylylated by acetyl-AMP”. X-ray diffraction, 2 ligands (AMP, SO4), 6 pockets (best druggability 0.66). MolNFT v1 #120421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GZW
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A7TUE6
- Ligands
- AMP, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 348 | 39% helix, 24% strand | A7TUE6 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 348 | 38% helix, 24% strand | A7TUE6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.66 | 0.77 | 38 | empty |
| 2 | 349 | 0.61 | 0.78 | 47 | AMP, SO4 |
| 3 | 252 | 0.55 | 0.77 | 32 | empty |
| 4 | 294 | 0.53 | 0.75 | 47 | AMP |
| 5 | 86 | 0.34 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5GZW · Crystal structure of AmpC BER adenylylated by acetyl-AMP · 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 A7TUE6
- Elsewhere: RCSB PDB 5GZW · PDBe 5GZW · UniProt A7TUE6
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