MolNFT v1 · #55259 · protein

Structure of phod

2YEQ · Alkaline phosphatase D: “Structure of phod”. X-ray diffraction, 4 ligands (NA, CA, FE), 11 pockets (best druggability 0.71). MolNFT v1 #55259 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YEQ
Type: protein
Length: 1,044 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alkaline phosphatase D
EC: 3.1.3.1
UniProt: P42251
Ligands: NA, CA, FE, PO4
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alkaline phosphatase D (EC 3.1.3.1)	protein	522	22% helix, 28% strand	P42251

Ligands and binding sites

NA · Sodium ion · metal · 6 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 43 copies · chains A, B
PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 30 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.71	0.81	60	EDO, PE5, NA
2	56	0.68	0.97	20	CA, PO4
3	58	0.67	0.96	19	CA, PO4
4	87	0.59	0.88	25	EDO
5	301	0.56	0.76	46	PE5

Interfaces

1 interface between chains.

A–B · 804 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2YEQ · Structure of PhoD · the same entry in another collection · chain A against A, TM-score 1.00
P42251 · AlphaFold monomer V2.0 prediction for alkaline phosphatase D (P42251) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P42251
Elsewhere: RCSB PDB 2YEQ · PDBe 2YEQ · UniProt P42251

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