Research workbench

Human atlastin-1 1-446, N440T, gppnhp

Analyse Human atlastin-1 1-446, N440T, gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IDP
Type: protein
Length: 1,665 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Atlastin-1
EC: 3.6.5.-
UniProt: Q8WXF7
Ligands: GNP, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Atlastin-1 (EC 3.6.5.-)	protein	416	47% helix, 16% strand	Q8WXF7
D	Atlastin-1 (EC 3.6.5.-)	protein	417	47% helix, 16% strand	Q8WXF7

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.87	0.93	85	GNP, MG
2	247	0.82	0.94	37	GNP, MG
3	309	0.82	0.92	55	GNP, MG
4	157	0.80	0.96	34	empty
5	165	0.80	0.96	33	empty

Interfaces

6 interfaces between chains.

A–B · 4103 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 4037 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 798 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 763 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 507 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

4IDP · human atlastin-1 1-446, N440T, GppNHp · the same entry in another collection · chain D against D, TM-score 1.00
Q8WXF7 · AlphaFold monomer V2.0 prediction for atlastin-1 (Q8WXF7) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q8WXF7
Elsewhere: RCSB PDB 4IDP · PDBe 4IDP · UniProt Q8WXF7

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