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Crystal structure of an asymmetric trimer of a glutamate transporter homologue (gltph)

Analyse Crystal structure of an asymmetric trimer of a glutamate transporter homologue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3V8G
Type: protein
Length: 2,421 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sodium-coupled L-aspartate transporter
UniProt: O59010
Ligands: ASP, NA
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Sodium-coupled L-aspartate transporter	protein	411	73% helix, 0% strand	O59010
B	Sodium-coupled L-aspartate transporter	protein	404	74% helix, 0% strand	O59010
C	Sodium-coupled L-aspartate transporter	protein	400	73% helix, 0% strand	O59010
E	Sodium-coupled L-aspartate transporter	protein	403	74% helix, 0% strand	O59010
F	Sodium-coupled L-aspartate transporter	protein	392	74% helix, 0% strand	O59010

Ligands and binding sites

ASP · Aspartic acid · ligand · 6 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 12 copies · chains A, B, 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	708	0.87	0.90	59	empty
2	710	0.86	0.89	64	empty
3	1195	0.82	0.83	116	empty
4	736	0.68	0.75	65	empty
5	430	0.66	0.79	56	empty

Interfaces

10 interfaces between chains.

B–C · 1141 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 1112 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1111 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1096 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1077 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3V8G · Crystal structure of an asymmetric trimer of a glutamate transporter homologue (GltPh) · the same entry in another collection · chain F against F, TM-score 1.00
O59010 · AlphaFold monomer V2.0 prediction for glutamate transporter homolog (O59010) · a predicted model of the same protein · chain C against A, TM-score 0.86

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 O59010
Elsewhere: RCSB PDB 3V8G · PDBe 3V8G · UniProt O59010

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