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Crystal structure of gltph in complex with L-asp

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

PDB: 2NWL
Type: protein
Length: 1,203 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate symport protein
UniProt: O59010
Ligands: PLM, ASP
Pockets: 12 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate symport protein	protein	402	77% helix, 0% strand	O59010
B	Glutamate symport protein	protein	398	76% helix, 0% strand	O59010
C	Glutamate symport protein	protein	403	76% helix, 0% strand	O59010

Ligands and binding sites

PLM · Palmitic acid · ligand · 3 copies · chains A, B, C
ASP · Aspartic acid · ligand · 3 copies · chains A, B, C

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

Pockets

12 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	603	0.88	0.93	44	empty
2	458	0.58	0.73	69	PLM
3	422	0.56	0.73	52	PLM
4	210	0.48	0.74	23	empty
5	165	0.41	0.73	31	PLM

Interfaces

3 interfaces between chains.

B–C · 1094 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1087 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1070 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2NWL · Crystal structure of GltPh in complex with L-Asp · the same entry in another collection · chain C against C, 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 2NWL · PDBe 2NWL · UniProt O59010

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