Research workbench
Promiscuous protein self-assembly as a function of protein stability
Analyse Promiscuous protein self-assembly as a function of protein stability in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NPO
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase tem; Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P62593, D3INY1
- Ligands
- MG
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase tem (EC 3.5.2.6) | protein | 263 | 43% helix, 17% strand | P62593 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 223 | 41% helix, 17% strand | D3INY1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.45 | 0.77 | 28 | empty |
| 2 | 92 | 0.34 | 0.75 | 21 | empty |
| 3 | 62 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 P62593
- Every structure of UniProt D3INY1
- Elsewhere: RCSB PDB 5NPO · PDBe 5NPO · UniProt P62593 · UniProt D3INY1
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