MolNFT v1 · #113248 · protein

Crystal structure of the extracellular domain of PEPT2

5A9I · Solute carrier family 15 member 2: “Crystal structure of the extracellular domain of PEPT2”. X-ray diffraction, 6 pockets (best druggability 0.57). MolNFT v1 #113248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5A9I
Type: protein
Length: 582 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Solute carrier family 15 member 2
UniProt: Q63424
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Solute carrier family 15 member 2	protein	194	0% helix, 61% strand	Q63424

Ligands and binding sites

CIT · Citric acid · additive · 2 copies · chains B
GOL · Glycerol · additive · chains B

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

Pockets

6 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	115	0.57	0.84	23	empty
2	203	0.54	0.78	27	empty
3	226	0.51	0.76	36	empty
4	222	0.48	0.74	30	empty
5	186	0.44	0.74	31	empty

Interfaces

3 interfaces between chains.

A–B · 746 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 256 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 98 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

5A9I · Crystal structure of the extracellular domain of PepT2 · the same entry in another collection · chain A against A, TM-score 1.00
Q63424 · AlphaFold monomer V2.0 prediction for solute carrier family 15 member 2 (Q63424) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q63424
Elsewhere: RCSB PDB 5A9I · PDBe 5A9I · UniProt Q63424

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