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Crystal structure of human atlastin-1 (residues 1-447) bound to GDP, crystal form 2

Analyse Crystal structure of human atlastin-1 (residues 1-447) bound to GDP, crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3Q5E
Type: protein
Length: 1,590 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: GDP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Atlastin-1 (EC 3.6.5.-)	protein	411	48% helix, 18% strand	Q8WXF7
C	Atlastin-1 (EC 3.6.5.-)	protein	409	39% helix, 18% strand	Q8WXF7
E	Atlastin-1 (EC 3.6.5.-)	protein	386	42% helix, 19% strand	Q8WXF7
G	Atlastin-1 (EC 3.6.5.-)	protein	384	42% helix, 18% strand	Q8WXF7

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, C, E, G
MG · Magnesium ion · metal · 4 copies · chains A, C, E, G

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	668	0.81	0.85	65	empty
2	643	0.79	0.84	60	empty
3	857	0.75	0.79	59	empty
4	842	0.74	0.78	55	empty
5	581	0.73	0.81	48	empty

Interfaces

4 interfaces between chains.

C–G · 1110 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 1027 Å² buried · 12 hydrogen bonds · protein-protein
E–G · 490 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 305 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3Q5E · crystal structure of human Atlastin-1 (residues 1-447) bound to GDP, crystal form 2 · the same entry in another collection · chain G against G, TM-score 1.00
Q8WXF7 · AlphaFold monomer V2.0 prediction for atlastin-1 (Q8WXF7) · a predicted model of the same protein · chain G against A, TM-score 0.71

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 3Q5E · PDBe 3Q5E · UniProt Q8WXF7

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