MolNFT v1 · #169246 · protein + RNA

Crystal structure of a stabilized pan ene bimolecular triplex with a gc-clamped polya tail, in complex with Fab-bl-3,6

6X5N · Light chain Fab bl-3 6: “Crystal structure of a stabilized pan ene bimolecular triplex with a gc-clamped polya tail, in complex with…”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.65). MolNFT v1 #169246 on…

PDB: 6X5N
Type: protein + RNA
Length: 982 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain Fab bl-3 6; Heavy chain Fab bl-3 6; Ggpan RNA (39-mer); GGCA9 RNA (12-mer)
Ligands: SO4
Pockets: 14 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
l, L	Light chain Fab bl-3 6	protein	215	6% helix, 51% strand	—
h, H	Heavy chain Fab bl-3 6	protein	225	7% helix, 48% strand	—
R, r	Ggpan RNA (39-mer)	rna	39	—	—
A, a	GGCA9 RNA (12-mer)	rna	12	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains l, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.65	0.95	23	empty
2	422	0.61	0.77	38	empty
3	499	0.60	0.74	56	empty
4	371	0.58	0.76	35	empty
5	106	0.52	0.83	24	empty

Interfaces

9 interfaces between chains.

H–L · 2117 Å² buried · 12 hydrogen bonds · protein-protein
l–h · 2061 Å² buried · 12 hydrogen bonds · protein-protein
R–A · 1139 Å² buried · 79 hydrogen bonds · nucleic-nucleic
r–a · 1111 Å² buried · 85 hydrogen bonds · nucleic-nucleic
H–R · 692 Å² buried · 20 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6X5N · Crystal structure of a stabilized PAN ENE bimolecular triplex with a GC-clamped polyA… · 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 6X5N · PDBe 6X5N

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