MolNFT v1 · #32515 · protein + DNA

Fitab bound to DNA

2BSQ · Trafficking protein B: “Fitab bound to DNA”. X-ray diffraction, 11 pockets (best druggability 0.58). MolNFT v1 #32515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BSQ
Type: protein + DNA
Length: 900 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trafficking protein B; Trafficking protein a; IR36, forward strand; IR36, reverse strand
UniProt: Q5F882, Q5F881
Pockets: 11 · best druggability 0.58

Structure

x-ray diffraction · 8 distinct chains · 58% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Trafficking protein B	protein	143	58% helix, 10% strand	Q5F882
B, D	Trafficking protein B	protein	140	55% helix, 11% strand	Q5F882
E	Trafficking protein a	protein	68	59% helix, 4% strand	Q5F881
F	Trafficking protein a	protein	64	61% helix, 5% strand	Q5F881
G	Trafficking protein a	protein	67	61% helix, 4% strand	Q5F881
H	Trafficking protein a	protein	63	60% helix, 5% strand	Q5F881
I	IR36, forward strand	dna	36	—	—
J	IR36, reverse strand	dna	36	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	374	0.58	0.76	31	empty
2	388	0.58	0.76	48	empty
3	169	0.51	0.78	25	empty
4	142	0.47	0.78	21	empty
5	96	0.43	0.79	24	empty

Interfaces

23 interfaces between chains.

I–J · 1555 Å² buried · 133 hydrogen bonds · nucleic-nucleic
F–G · 1441 Å² buried · 32 hydrogen bonds · protein-protein
E–H · 1425 Å² buried · 26 hydrogen bonds · protein-protein
A–E · 1366 Å² buried · 25 hydrogen bonds · protein-protein
C–G · 1356 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2BSQ · FitAB bound to DNA · the same entry in another collection · chain J against J, TM-score 1.00
Q5F882 · AlphaFold monomer V2.0 prediction for toxin fitb (Q5F882) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q5F882
Every structure of UniProt Q5F881
Elsewhere: RCSB PDB 2BSQ · PDBe 2BSQ · UniProt Q5F882 · UniProt Q5F881

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