MolNFT v1 · #104416 · protein + RNA

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab

4Q9R · Fab BL3-6, heavy chain: “Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab”. X-ray diffraction, 2 ligands (2ZY, K), 7 pockets (best druggability 0.73). MolNFT v1 #104416 on GenesisL1: 3D…

PDB: 4Q9R
Type: protein + RNA
Length: 521 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab BL3-6, heavy chain; Fab BL3-6, light chain; Spinach RNA aptamer
Ligands: 2ZY, K
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab BL3-6, heavy chain	protein	223	9% helix, 49% strand	—
L	Fab BL3-6, light chain	protein	214	6% helix, 51% strand	—
R	Spinach RNA aptamer	rna	84	—	—

Ligands and binding sites

2ZY · (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one · ligand · chains R
K · Potassium ion · metal · chains R

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	850	0.73	0.78	59	2ZY
2	494	0.60	0.74	49	empty
3	249	0.56	0.78	36	empty
4	383	0.55	0.75	24	empty
5	382	0.52	0.73	24	empty

Interfaces

3 interfaces between chains.

H–L · 1965 Å² buried · 14 hydrogen bonds · protein-protein
H–R · 707 Å² buried · 14 hydrogen bonds · protein-nucleic
L–R · 141 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).

Compared structures

4Q9R · Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with… · the same entry in another collection · chain H against H, 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 4Q9R · PDBe 4Q9R

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