MolNFT v1 · #169676 · protein + RNA

Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety

6XJW · Self-alkylating ribozyme (58-mer): “Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety”. X-ray diffraction, 1 ligand (97C), 15 pockets (best druggability 0.80). MolNFT v1 #169676 on GenesisL1: 3D…

PDB: 6XJW
Type: protein + RNA
Length: 999 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Self-alkylating ribozyme (58-mer); Fab havx heavy chain; Fab havx light chain
Ligands: 97C
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Self-alkylating ribozyme (58-mer)	rna	58	—	—
C	Fab havx heavy chain	protein	227	8% helix, 52% strand	—
D, L	Fab havx light chain	protein	214	7% helix, 50% strand	—
H	Fab havx heavy chain	protein	228	10% helix, 50% strand	—

Ligands and binding sites

97C · 2-{[(4R)-4-hydroxyhexyl]oxy}ethyl pentanoate · ligand · 2 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	976	0.80	0.82	83	empty
2	340	0.63	0.80	32	empty
3	317	0.58	0.77	20	empty
4	247	0.55	0.79	18	empty
5	353	0.54	0.74	49	empty

Interfaces

11 interfaces between chains.

C–D · 1908 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 1852 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 600 Å² buried · 19 hydrogen bonds · protein-nucleic
A–L · 591 Å² buried · 19 hydrogen bonds · protein-nucleic
B–C · 561 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

6XJW · Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety · 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 6XJW · PDBe 6XJW

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