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Crystal structure of gltph in complex with L-aspartate and sodium ions

Analyse Crystal structure of gltph in complex with L-aspartate and sodium ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NWX
Type: protein
Length: 1,197 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 425AA long hypothetical proton glutamate symport protein
UniProt: O59010
Ligands: ASP, PLM, NA
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	425AA long hypothetical proton glutamate symport protein	protein	400	77% helix, 0% strand	O59010
B	425AA long hypothetical proton glutamate symport protein	protein	396	79% helix, 0% strand	O59010
C	425AA long hypothetical proton glutamate symport protein	protein	401	76% helix, 0% strand	O59010

Ligands and binding sites

ASP · Aspartic acid · ligand · 3 copies · chains A, B, C
PLM · Palmitic acid · ligand · 3 copies · chains A, B, C
NA · Sodium ion · metal · 6 copies · chains A, B, C

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	648	0.87	0.91	43	empty
2	391	0.56	0.74	54	PLM
3	364	0.55	0.73	46	PLM
4	214	0.48	0.74	35	empty
5	203	0.44	0.73	28	PLM

Interfaces

3 interfaces between chains.

A–C · 1084 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1079 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1068 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2NWX · Crystal structure of GltPh in complex with L-aspartate and sodium ions · the same entry in another collection · chain A against A, TM-score 1.00
O59010 · AlphaFold monomer V2.0 prediction for glutamate transporter homolog (O59010) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 2NWX · PDBe 2NWX · UniProt O59010

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