Research workbench

Rip-radiation-damage induced phasing

Analyse Rip-radiation-damage induced phasing in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1N7B
Type: RNA
Length: 48 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
Ligands: SPM, K

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	RNA/DNA (5'-R(U)-D(P(BGM))-R(PAPGPGPU)-3')	rna	6	—	—

Ligands and binding sites

SPM · Spermine · ligand · 2 copies · chains A, B, F, H
K · Potassium ion · metal · 9 copies · chains A, C, D, H, B, E, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

24 interfaces between chains.

F–H · 380 Å² buried · 11 hydrogen bonds · nucleic-nucleic
C–G · 378 Å² buried · 11 hydrogen bonds · nucleic-nucleic
A–B · 375 Å² buried · 13 hydrogen bonds · nucleic-nucleic
D–E · 374 Å² buried · 12 hydrogen bonds · nucleic-nucleic
D–H · 264 Å² buried · 16 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

1N7B · RIP-Radiation-damage Induced Phasing · the same entry in another collection · chain A against A, 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 1N7B · PDBe 1N7B

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