MolNFT v1 · #179011 · protein

Structure of the nact-PF2 complex

7JSJ · Solute carrier family 13 member 5: “Structure of the nact-PF2 complex”. Electron microscopy, 3 ligands (X3M, NAG, NA), 13 pockets (best druggability 0.67). MolNFT v1 #179011 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7JSJ
Type: protein
Length: 936 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Solute carrier family 13 member 5
UniProt: Q86YT5
Ligands: X3M, NAG, NA
Pockets: 13 · best druggability 0.67

Structure

electron microscopy · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Solute carrier family 13 member 5	protein	468	70% helix, 0% strand	Q86YT5

Ligands and binding sites

X3M · (2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
NA · Sodium ion · metal · 4 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	438	0.67	0.79	44	X3M
2	493	0.67	0.78	40	X3M
3	182	0.58	0.80	22	empty
4	178	0.57	0.80	20	empty
5	138	0.56	0.81	24	empty

Interfaces

1 interface between chains.

A–B · 2367 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 glycan (N-glycosylation).

Compared structures

7JSJ · Structure of the NaCT-PF2 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q86YT5 · AlphaFold monomer V2.0 prediction for solute carrier family 13 member 5 (Q86YT5) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q86YT5
Elsewhere: RCSB PDB 7JSJ · PDBe 7JSJ · UniProt Q86YT5

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