MolNFT v1 · #76988 · RNA
Crystal structure of gcggcggc duplex
3R1C · RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3'): “Crystal structure of gcggcggc duplex”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.69). MolNFT v1 #76988 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3R1C
- Type
- RNA
- Length
- 288 nucleotides
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, Y, T, U, W, X, V, Z, a, b, c, d, e, f, g, h, i, j | RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3') | rna | 8 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains S, W, X, b, c, d, e
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 719 | 0.69 | 0.77 | 37 | empty |
| 2 | 317 | 0.68 | 0.83 | 28 | empty |
| 3 | 78 | 0.31 | 0.74 | 12 | empty |
| 4 | 51 | 0.24 | 0.73 | 10 | empty |
Interfaces
77 interfaces between chains.
- V–Z · 404 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- O–P · 403 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- E–F · 403 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- g–h · 402 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- G–H · 401 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Compared structures
- 3R1C · Crystal structure of GCGGCGGC duplex · 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
- Elsewhere: RCSB PDB 3R1C · PDBe 3R1C
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