Research workbench
Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A
Analyse Cryogenic crystal structure of barnase A43C/S80C bound to barstar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PQK
- Type
- protein
- Length
- 394 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease; Barstar
- EC
- 3.1.27.-
- UniProt
- P00648, P11540
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribonuclease (EC 3.1.27.-) | protein | 108 | 22% helix, 23% strand | P00648 |
| B | Barstar | protein | 90 | 47% helix, 19% strand | P11540 |
| D | Barstar | protein | 88 | 49% helix, 17% strand | P11540 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.58 | 0.78 | 32 | empty |
| 2 | 150 | 0.47 | 0.77 | 24 | empty |
| 3 | 81 | 0.45 | 0.81 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–D · 855 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 816 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 345 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 187 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PQK · Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A · the same entry in another collection · chain A against A, TM-score 1.00
- P11540 · AlphaFold monomer V2.0 prediction for barstar (P11540) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 6PQK · PDBe 6PQK · UniProt P00648 · UniProt P11540
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