MolNFT v1 · #14499 · protein
Beta-lactam synthetase complexed with ATP
1MB9: “Beta-lactam synthetase complexed with ATP”. X-ray diffraction, 4 ligands (ATP, POP, AMP), 13 pockets (best druggability 0.74). MolNFT v1 #14499 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1MB9
- Type
- protein
- Length
- 982 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactam synthetase
- UniProt
- Q9R8E3
- Ligands
- ATP, POP, AMP, MG
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactam synthetase | protein | 485 | 39% helix, 20% strand | Q9R8E3 |
| B | Beta-lactam synthetase | protein | 497 | 39% helix, 20% strand | Q9R8E3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.74 | 0.80 | 57 | empty |
| 2 | 797 | 0.73 | 0.78 | 74 | MG, ATP |
| 3 | 611 | 0.71 | 0.79 | 78 | MG, POP, AMP, ATP |
| 4 | 181 | 0.55 | 0.80 | 36 | empty |
| 5 | 174 | 0.50 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1321 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1MB9 · Beta-lactam synthetase complexed with ATP · 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 Q9R8E3
- Elsewhere: RCSB PDB 1MB9 · PDBe 1MB9 · UniProt Q9R8E3
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