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Kidney bean purple acid phosphatase

Analyse Kidney bean purple acid phosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KBP
Type: protein
Length: 1,696 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purple acid phosphatase
EC: 3.1.3.2
UniProt: P80366
Ligands: NAG, FE, ZN
Pockets: 13 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Purple acid phosphatase (EC 3.1.3.2)	protein	424	16% helix, 30% strand	P80366

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D, B, C
FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

13 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	405	0.68	0.80	38	empty
2	427	0.65	0.78	35	empty
3	196	0.47	0.75	28	empty
4	68	0.45	0.82	15	empty
5	193	0.45	0.74	26	empty

Interfaces

3 interfaces between chains.

B–C · 1478 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 470 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 182 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

1KBP · Kidney bean purple acid phosphatase · the same entry in another collection · chain A against A, TM-score 1.00
P80366 · AlphaFold monomer V2.0 prediction for FE(3+)-ZN(2+) purple acid phosphatase (P80366) · 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 P80366
Elsewhere: RCSB PDB 1KBP · PDBe 1KBP · UniProt P80366

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