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Crystal structure of the catalytic core of an RNA polymerase ribozyme complexed with an antigen binding antibody fragment

Analyse Crystal structure of the catalytic core of an RNA polymerase ribozyme complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IVK
Type: protein + RNA
Length: 1,130 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; Class I ligase product
Ligands: MG, CD, CL
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, B	Fab light chain	protein	213	7% helix, 51% strand	—
H, A	Fab heavy chain	protein	224	11% helix, 50% strand	—
M, C	Class I ligase product	rna	128	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 33 copies · chains L, B, M, C
CD · Cadmium ion · metal · 2 copies · chains L, H, B, A
CL · Chloride ion · ion · 2 copies · chains L, H, B, A

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.70	0.80	39	empty
2	541	0.69	0.80	39	empty
3	428	0.69	0.81	54	CL, MG
4	390	0.68	0.82	49	CL, MG
5	390	0.61	0.78	28	MG

Interfaces

8 interfaces between chains.

L–H · 1998 Å² buried · 18 hydrogen bonds · protein-protein
B–A · 1993 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 725 Å² buried · 14 hydrogen bonds · protein-nucleic
H–M · 718 Å² buried · 14 hydrogen bonds · protein-nucleic
B–C · 478 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3IVK · Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an… · the same entry in another collection · chain L against L, 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 3IVK · PDBe 3IVK

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