Research workbench
Crystal structure of a plectonemic RNA supercoil
Analyse Crystal structure of a plectonemic RNA supercoil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EYA
- Type
- protein + RNA
- Length
- 1,336 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N utilization substance protein B homolog; RNA…
- UniProt
- O66530
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | N utilization substance protein B homolog | protein | 138 | 79% helix, 0% strand | O66530 |
| B, D, F, H | N utilization substance protein B homolog | protein | 136 | 80% helix, 0% strand | O66530 |
| a, c, e, g, i, j, h, f, d, b, k, m, o, q, s, t, r, p, n, l | RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3') | rna | 12 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, D, F, H
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.69 | 0.74 | 46 | empty |
| 2 | 660 | 0.67 | 0.77 | 46 | empty |
| 3 | 669 | 0.67 | 0.77 | 46 | empty |
| 4 | 606 | 0.63 | 0.74 | 37 | GOL |
| 5 | 634 | 0.63 | 0.74 | 47 | GOL |
Interfaces
77 interfaces between chains.
- k–l · 516 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- e–f · 514 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- q–r · 513 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- i–j · 511 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- a–b · 507 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 4EYA · Crystal Structure of a Plectonemic RNA Supercoil · the same entry in another collection · chain e against e, 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 O66530
- Elsewhere: RCSB PDB 4EYA · PDBe 4EYA · UniProt O66530
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