Research workbench
Structure of bacteriophage coat protein-loop RNA complex
Analyse Structure of bacteriophage coat protein-loop RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZDK
- Type
- protein + RNA
- Length
- 425 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (MS2 protein capsid); RNA (5'- R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP…
- UniProt
- P03612
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (MS2 protein capsid) | protein | 129 | 19% helix, 48% strand | P03612 |
| R, S | RNA (5'- R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U )-3') | rna | 19 | — | — |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.76 | 0.78 | 126 | empty |
| 2 | 369 | 0.59 | 0.76 | 32 | empty |
| 3 | 461 | 0.58 | 0.74 | 30 | empty |
| 4 | 457 | 0.57 | 0.74 | 24 | empty |
| 5 | 60 | 0.32 | 0.77 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–C · 570 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 4 hydrogen bonds · protein-protein
- C–S · 451 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–R · 428 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1ZDK · Structure of bacteriophage coat protein-loop RNA complex · the same entry in another collection · chain B against B, 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 1ZDK · PDBe 1ZDK · UniProt P03612
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