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Crystal structure of a self-alkylating ribozyme - apo form

Analyse Crystal structure of a self-alkylating ribozyme - apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XJZ
Type: protein + RNA
Length: 988 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
Pockets: 15 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Self-alkylating ribozyme (58-mer)	rna	58	—	—
C, H	Fab havx heavy chain	protein	224	6% helix, 52% strand	—
D, L	Fab havx light chain	protein	212	6% helix, 50% strand	—

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.65	0.79	37	empty
2	382	0.64	0.79	33	empty
3	331	0.61	0.79	19	empty
4	299	0.58	0.78	17	empty
5	310	0.53	0.74	39	empty

Interfaces

7 interfaces between chains.

H–L · 1768 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1732 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 585 Å² buried · 22 hydrogen bonds · protein-nucleic
A–L · 581 Å² buried · 17 hydrogen bonds · protein-nucleic
A–H · 551 Å² buried · 11 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6XJZ · Crystal structure of a self-alkylating ribozyme - apo form · 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 6XJZ · PDBe 6XJZ

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