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Crystal Structure of GltPh R397C in complex with L-Serine

Analyse Crystal Structure of GltPh R397C in complex with L-Serine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BMI
Type: protein
Length: 1,200 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.9
Source: Pyrococcus horikoshii
Molecule: Glutamate transporter homolog
UniProt: O59010
Ligands: SER, NA
Pockets: 15 · best druggability 0.88

Structure

x-ray diffraction · resolution 3.9 · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutamate transporter homolog	protein	396	78% helix, 0% strand	O59010
C	Glutamate transporter homolog	protein	408	76% helix, 0% strand	O59010

Ligands and binding sites

SER · Serine · ligand · 3 copies · chains A, B, C
NA · Sodium ion · metal · 4 copies · chains A, B, C

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

Pockets

15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	644	0.88	0.91	39	empty
2	432	0.58	0.74	43	empty
3	213	0.49	0.75	27	empty
4	189	0.47	0.75	27	SER
5	191	0.45	0.73	27	empty

Interfaces

3 interfaces between chains.

B–C · 1145 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1128 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1113 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6BMI · Crystal structure of gltph R397C in complex with L-serine · 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 0.96

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 6BMI · PDBe 6BMI · UniProt O59010

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