MolNFT v1 · #104415 · protein + RNA

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

4Q9Q · Fab BL3-6, heavy chain: “Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab”. X-ray diffraction, 3 ligands (2ZZ, MG, K), 6 pockets (best druggability 0.71). MolNFT v1 #104415 on GenesisL1: 3D…

PDB: 4Q9Q
Type: protein + RNA
Length: 524 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: 2ZZ, MG, K
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab BL3-6, heavy chain	protein	225	10% helix, 48% strand	—
L	Fab BL3-6, light chain	protein	215	5% helix, 50% strand	—
R	Spinach RNA aptamer	rna	84	—	—

Ligands and binding sites

2ZZ · (5Z)-5-(3-bromobenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one · ligand · chains R
MG · Magnesium ion · metal · chains R
K · Potassium ion · metal · chains R

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	819	0.71	0.78	57	MG, 2ZZ
2	479	0.60	0.75	49	empty
3	141	0.56	0.82	28	empty
4	357	0.53	0.75	24	empty
5	357	0.50	0.73	23	empty

Interfaces

3 interfaces between chains.

H–L · 2039 Å² buried · 14 hydrogen bonds · protein-protein
H–R · 688 Å² buried · 15 hydrogen bonds · protein-nucleic
L–R · 149 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, nucleotide modification).

Compared structures

4Q9Q · Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab · 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 4Q9Q · PDBe 4Q9Q

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