Research workbench
RNA stemloop operator from bacteriophage qbeta complexed with an N87S, E89K mutant MS2 capsid
Analyse RNA stemloop operator from bacteriophage qbeta complexed with an N87S, E89K… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B2D
- Type
- protein + RNA
- Length
- 399 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP *AP*U)-3'; Coat protein
- UniProt
- P03612
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP *AP*U)-3' | rna | 9 | — | — |
| S | 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP *AP*U)-3' | rna | 3 | — | — |
| A, B, C | Coat protein | protein | 129 | 21% helix, 46% strand | P03612 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.63 | 0.77 | 40 | empty |
| 2 | 462 | 0.61 | 0.75 | 48 | empty |
| 3 | 119 | 0.42 | 0.77 | 18 | empty |
| 4 | 64 | 0.31 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3290 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 6 hydrogen bonds · protein-protein
- R–A · 341 Ų buried · 7 hydrogen bonds · protein-nucleic
- S–C · 340 Ų buried · 9 hydrogen bonds · protein-nucleic
- R–B · 264 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 2B2D · RNA stemloop operator from bacteriophage QBETA complexed with an N87S,E89K mutant MS2… · the same entry in another collection · chain R against R, 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 P03612
- Elsewhere: RCSB PDB 2B2D · PDBe 2B2D · UniProt P03612
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