Research workbench
The modular architecture of protein-protein binding site
Analyse The modular architecture of protein-protein binding site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XXM
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase tem; Beta-lactamase inhibitory protein
- EC
- 3.5.2.6
- UniProt
- P62593, P35804
- Ligands
- CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase tem (EC 3.5.2.6) | protein | 263 | 45% helix, 16% strand | P62593 |
| C, D | Beta-lactamase inhibitory protein | protein | 165 | 21% helix, 36% strand | P35804 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, D
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 | 342 | 0.79 | 0.89 | 51 | empty |
| 2 | 354 | 0.78 | 0.88 | 56 | empty |
| 3 | 115 | 0.61 | 0.87 | 24 | empty |
| 4 | 134 | 0.53 | 0.81 | 27 | empty |
| 5 | 81 | 0.40 | 0.78 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–D · 1124 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1116 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1XXM · The modular architecture of protein-protein binding site · the same entry in another collection · chain D against D, TM-score 1.00
- P35804 · AlphaFold monomer V2.0 prediction for beta-lactamase inhibitory protein (P35804) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P62593 · AlphaFold monomer V2.0 prediction for beta-lactamase tem (P62593) · a predicted model of the same protein · 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 P62593
- Every structure of UniProt P35804
- Elsewhere: RCSB PDB 1XXM · PDBe 1XXM · UniProt P62593 · UniProt P35804
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