MolNFT v1 · #169670 · protein + RNA

Crystal structure of a self-alkylating ribozyme - alkylated form with biotinylated epoxide substrate

6XJQ · Self-alkylating ribozyme (58-mer): “Crystal structure of a self-alkylating ribozyme - alkylated form with biotinylated epoxide substrate”. X-ray diffraction, 1 ligand (V4J), 14 pockets (best druggability 0.78). MolNFT v1 #169670 on…

PDB: 6XJQ
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: V4J
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 50% 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	9% helix, 51% 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

V4J · 2-{[(4R)-4-hydroxyhexyl]oxy}ethyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate · ligand · 2 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1082	0.78	0.80	88	empty
2	356	0.64	0.80	35	empty
3	326	0.58	0.77	19	empty
4	281	0.58	0.79	17	empty
5	300	0.56	0.76	36	empty

Interfaces

10 interfaces between chains.

C–D · 1847 Å² buried · 13 hydrogen bonds · protein-protein
H–L · 1816 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 605 Å² buried · 18 hydrogen bonds · protein-nucleic
A–L · 591 Å² buried · 18 hydrogen bonds · protein-nucleic
B–C · 566 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

6XJQ · Crystal structure of a self-alkylating ribozyme - alkylated form with biotinylated… · 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 6XJQ · PDBe 6XJQ

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