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Crystal structure of crosslinked gltph V216C-M385C mutant

Analyse Crystal structure of crosslinked gltph V216C-M385C mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3V8F
Type: protein
Length: 1,231 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sodium-coupled L-aspartate transporter
UniProt: O59010
Ligands: ASP, NA, HG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Sodium-coupled L-aspartate transporter	protein	410	71% helix, 0% strand	O59010
B	Sodium-coupled L-aspartate transporter	protein	411	70% helix, 0% strand	O59010

Ligands and binding sites

ASP · Aspartic acid · ligand · 3 copies · chains A, B, C
NA · Sodium ion · metal · 6 copies · chains A, B, C
HG · Mercury (II) ion · metal · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	800	0.89	0.91	40	empty
2	345	0.65	0.80	47	HG
3	440	0.63	0.77	42	empty
4	395	0.61	0.77	42	empty
5	423	0.61	0.76	37	empty

Interfaces

3 interfaces between chains.

B–C · 1154 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1151 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1146 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3V8F · Crystal structure of crosslinked GltPh V216C-M385C mutant · 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 C against A, TM-score 0.64

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 3V8F · PDBe 3V8F · UniProt O59010

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