MolNFT v1 · #19227 · protein

Amino terminal domain of the N-ethylmaleimide sensitive fusion protein (nsf)

1QDN · Protein (N-ethylmaleimide sensitive fusion protein (nsf)): “Amino terminal domain of the N-ethylmaleimide sensitive fusion protein (nsf)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.63). MolNFT v1 #19227 on…

PDB: 1QDN
Type: protein
Length: 568 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (N-ethylmaleimide sensitive fusion protein (nsf))
UniProt: P18708
Ligands: SO4
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein (N-ethylmaleimide sensitive fusion protein (nsf))	protein	189	15% helix, 43% strand	P18708
C	Protein (N-ethylmaleimide sensitive fusion protein (nsf))	protein	190	14% helix, 44% strand	P18708

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	216	0.63	0.82	35	empty
2	243	0.62	0.81	37	SO4
3	206	0.61	0.82	28	empty
4	141	0.58	0.83	30	empty
5	123	0.37	0.73	27	SO4

Interfaces

3 interfaces between chains.

A–B · 697 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 642 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 613 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (additive adduct).

Compared structures

1QDN · Amino terminal domain of the N-ethylmaleimide sensitive fusion protein (nsf) · the same entry in another collection · chain A against A, TM-score 1.00
P18708 · AlphaFold monomer V2.0 prediction for vesicle-fusing ATPase (P18708) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P18708
Elsewhere: RCSB PDB 1QDN · PDBe 1QDN · UniProt P18708

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