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Stalled ftsk motor domain bound to dsdna end

Analyse Stalled ftsk motor domain bound to dsdna end in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T8O
Type: protein + DNA
Length: 2,400 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA translocase ftsk; Dsdna substrate
UniProt: Q9I0M3
Ligands: ADP
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 8 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA translocase ftsk	protein	395	35% helix, 18% strand	Q9I0M3
B	DNA translocase ftsk	protein	392	36% helix, 17% strand	Q9I0M3
C	DNA translocase ftsk	protein	398	35% helix, 19% strand	Q9I0M3
D	DNA translocase ftsk	protein	396	37% helix, 19% strand	Q9I0M3
E	DNA translocase ftsk	protein	396	34% helix, 18% strand	Q9I0M3
F	DNA translocase ftsk	protein	397	38% helix, 17% strand	Q9I0M3
G	Dsdna substrate	dna	13	—	—
H	Dsdna substrate	dna	13	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	865	0.80	0.83	102	empty
2	892	0.76	0.80	75	empty
3	480	0.75	0.84	53	empty
4	430	0.73	0.83	66	empty
5	685	0.70	0.78	74	ADP

Interfaces

17 interfaces between chains.

A–F · 1374 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1178 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 1157 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 1119 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 1109 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6T8O · Stalled FtsK motor domain bound to dsDNA end · the same entry in another collection · chain H against H, TM-score 1.00
Q9I0M3 · AlphaFold monomer V2.0 prediction for DNA translocase ftsk (Q9I0M3) · a predicted model of the same protein · chain F against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9I0M3
Elsewhere: RCSB PDB 6T8O · PDBe 6T8O · UniProt Q9I0M3

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