Research workbench

Nsf-D1D2 part in the whole 20S complex

Analyse Nsf-D1D2 part in the whole 20S complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IP2
Type: protein
Length: 3,120 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vesicle-fusing ATPase
EC: 3.6.4.6
UniProt: P18708
Ligands: ATP
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 32% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, C, D, E, F, A	Vesicle-fusing ATPase (EC 3.6.4.6)	protein	520	32% helix, 11% strand	P18708

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains B, A, 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	476	0.86	0.92	58	ATP
2	929	0.85	0.87	113	ATP
3	513	0.85	0.91	61	ATP
4	570	0.85	0.90	63	ATP
5	658	0.84	0.89	69	ATP

Interfaces

7 interfaces between chains.

B–C · 3974 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 3816 Å² buried · 34 hydrogen bonds · protein-protein
D–E · 3815 Å² buried · 30 hydrogen bonds · protein-protein
E–F · 3551 Å² buried · 39 hydrogen bonds · protein-protein
B–A · 3271 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

6IP2 · NSF-D1D2 part in the whole 20S complex · the same entry in another collection · chain D against D, TM-score 1.00
P18708 · AlphaFold monomer V2.0 prediction for vesicle-fusing ATPase (P18708) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 6IP2 · PDBe 6IP2 · UniProt P18708

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