MolNFT v1 · #31669 · protein + RNA
RNA stemloop operator from bacteriophage qbeta complexed with an N87S, E89K mutant MS2 capsid
2B2D · 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP…: “RNA stemloop operator from bacteriophage qbeta complexed with an N87S, E89K mutant MS2 capsid”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #31669…
- 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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