MolNFT v1 · #127190 · protein

The structure of PST2P from saccharomyces cerevisiae

5MP4 · Protoplast secreted protein 2: “The structure of PST2P from saccharomyces cerevisiae”. X-ray diffraction, 1 ligand (PO4), 17 pockets (best druggability 0.84). MolNFT v1 #127190 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5MP4
Type: protein
Length: 1,576 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protoplast secreted protein 2
UniProt: Q12335
Ligands: PO4
Pockets: 17 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Protoplast secreted protein 2	protein	197	40% helix, 20% strand	Q12335

Ligands and binding sites

PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	710	0.84	0.87	93	PO4
2	175	0.82	0.97	33	empty
3	165	0.82	0.97	35	empty
4	149	0.82	0.98	32	empty
5	149	0.81	0.98	34	empty

Interfaces

15 interfaces between chains.

A–B · 1224 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 1219 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 1218 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 1216 Å² buried · 9 hydrogen bonds · protein-protein
F–H · 908 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5MP4 · The structure of Pst2p from Saccharomyces cerevisiae · the same entry in another collection · chain H against H, TM-score 1.00
Q12335 · AlphaFold monomer V2.0 prediction for protoplast secreted protein 2 (Q12335) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q12335
Elsewhere: RCSB PDB 5MP4 · PDBe 5MP4 · UniProt Q12335

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