MolNFT v1 · #117171 · protein + RNA

Specific recognition of a single-stranded RNA sequence by an engineered synthetic antibody fragment

5E08 · Fab heavy chain: “Specific recognition of a single-stranded RNA sequence by an engineered synthetic antibody fragment”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #117171 on GenesisL1: 3D structure, binding…

PDB: 5E08
Type: protein + RNA
Length: 456 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; RNA
Pockets: 3 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	229	9% helix, 50% strand	—
L	Fab light chain	protein	215	6% helix, 50% strand	—
N	RNA	rna	12	—	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.63	0.74	66	empty
2	249	0.55	0.77	36	empty
3	77	0.30	0.73	17	empty

Interfaces

3 interfaces between chains.

H–L · 2028 Å² buried · 16 hydrogen bonds · protein-protein
H–N · 779 Å² buried · 21 hydrogen bonds · protein-nucleic
L–N · 237 Å² buried · 4 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5E08 · Specific Recognition of a Single-stranded RNA Sequence by an Engineered Synthetic… · 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 5E08 · PDBe 5E08

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