MolNFT v1 · #95011 · protein

Human atlastin-1 1-446, C-HIS6, gppnhp

4IDN: “Human atlastin-1 1-446, C-HIS6, gppnhp”. X-ray diffraction, 2 ligands (GNP, MG), 9 pockets (best druggability 0.87). MolNFT v1 #95011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4IDN
Type: protein
Length: 840 residues
Chains: 2
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: 9 · best druggability 0.87

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Atlastin-1 (EC 3.6.5.-)	protein	417	47% helix, 16% strand	Q8WXF7
B	Atlastin-1 (EC 3.6.5.-)	protein	423	48% helix, 16% strand	Q8WXF7

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.87	0.93	83	GNP, MG
2	169	0.81	0.97	34	empty
3	260	0.69	0.84	32	empty
4	561	0.64	0.75	61	empty
5	337	0.54	0.74	30	empty

Interfaces

1 interface between chains.

A–B · 4042 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

4IDN · Human atlastin-1 1-446, C-his6, GppNHp · the same entry in another collection · chain A against A, TM-score 1.00
Q8WXF7 · AlphaFold monomer V2.0 prediction for atlastin-1 (Q8WXF7) · a predicted model of the same protein · chain A 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 4IDN · PDBe 4IDN · UniProt Q8WXF7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.