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Crystal structure of almond PRU1 protein

Analyse Crystal structure of almond PRU1 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FZ3
Type: protein
Length: 2,394 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prunin
UniProt: Q43607
Ligands: NA, CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E	Prunin	protein	388	16% helix, 38% strand	Q43607
B, C, F	Prunin	protein	410	18% helix, 36% strand	Q43607

Ligands and binding sites

NA · Sodium ion · metal · 9 copies · chains A, B, D, C, E, F
CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 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	389	0.85	0.94	43	CA
2	364	0.84	0.94	43	CA
3	321	0.84	0.95	42	CA
4	802	0.80	0.83	84	empty
5	756	0.79	0.83	84	empty

Interfaces

15 interfaces between chains.

A–F · 3096 Å² buried · 69 hydrogen bonds · protein-protein
C–D · 3064 Å² buried · 72 hydrogen bonds · protein-protein
B–E · 3010 Å² buried · 72 hydrogen bonds · protein-protein
A–B · 2890 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 2824 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3FZ3 · Crystal Structure of almond Pru1 protein · the same entry in another collection · chain F against F, TM-score 1.00
Q43607 · AlphaFold monomer V2.0 prediction for prunin 1 pru du 6 (Q43607) · 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 Q43607
Elsewhere: RCSB PDB 3FZ3 · PDBe 3FZ3 · UniProt Q43607

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