Research workbench
Water-mediate interaction at aprotein-protein interface
Analyse Water-mediate interaction at aprotein-protein interface in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X1U
- Type
- protein
- Length
- 596 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Bacillus amyloliquefaciens
- Molecule
- Ribonuclease; Barstar
- EC
- 3.1.27.-
- UniProt
- P00648, P11540
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease (EC 3.1.27.-) | protein | 110 | 22% helix, 23% strand | P00648 |
| C | Ribonuclease (EC 3.1.27.-) | protein | 109 | 23% helix, 23% strand | P00648 |
| D, E, F | Barstar | protein | 89 | 48% helix, 18% strand | P11540 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.59 | 0.76 | 44 | empty |
| 2 | 384 | 0.56 | 0.75 | 38 | empty |
| 3 | 96 | 0.48 | 0.81 | 24 | empty |
| 4 | 164 | 0.47 | 0.76 | 24 | empty |
| 5 | 125 | 0.46 | 0.78 | 23 | empty |
Interfaces
7 interfaces between chains.
- B–E · 862 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 821 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 816 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 282 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1X1U · Water-mediate interaction at aprotein-protein interface · the same entry in another collection · chain F against F, TM-score 1.00
- P00648 · AlphaFold monomer V2.0 prediction for ribonuclease (P00648) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P11540 · AlphaFold monomer V2.0 prediction for barstar (P11540) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P00648
- Every structure of UniProt P11540
- Elsewhere: RCSB PDB 1X1U · PDBe 1X1U · UniProt P00648 · UniProt P11540
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