MolNFT v1 · #67814 · protein + RNA

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

3IVK · Fab light chain: “Crystal structure of the catalytic core of an RNA polymerase ribozyme complexed with an antigen binding…”. X-ray diffraction, 3 ligands (MG, CD, CL), 20 pockets (best druggability 0.70). MolNFT v1 #67814 on…

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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