MolNFT v1 · #191234 · protein + DNA + RNA

Iscb and wrna bound to target DNA (locked state)

8CTL: “Iscb and wrna bound to target DNA (locked state)”. Electron microscopy, 14 pockets (best druggability 0.84). MolNFT v1 #191234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8CTL
Type: protein + DNA + RNA
Length: 634 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Iscb; RNA (222-mer); DNA target strand; DNA non-target strand
Pockets: 14 · best druggability 0.84

Structure

electron microscopy · 4 distinct chains · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Iscb	protein	401	27% helix, 24% strand	—
C	RNA (222-mer)	rna	184	—	—
A	DNA target strand	dna	29	—	—
B	DNA non-target strand	dna	20	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1035	0.84	0.85	90	empty
2	704	0.75	0.81	59	empty
3	751	0.73	0.79	71	empty
4	326	0.58	0.77	34	empty
5	161	0.56	0.82	22	empty

Interfaces

6 interfaces between chains.

D–C · 6217 Å² buried · 147 hydrogen bonds · protein-nucleic
D–A · 1492 Å² buried · 21 hydrogen bonds · protein-nucleic
C–A · 782 Å² buried · 75 hydrogen bonds · nucleic-nucleic
D–B · 666 Å² buried · 8 hydrogen bonds · protein-nucleic
A–B · 626 Å² buried · 62 hydrogen bonds · nucleic-nucleic

Compared structures

8CTL · IscB and wRNA bound to Target DNA (locked state) · the same entry in another collection · chain D against D, 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 8CTL · PDBe 8CTL

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