MolNFT v1 · #155175 · protein

Crystal structure of plant phospholipase D alpha

6KZ9 · Phospholipase D alpha 1: “Crystal structure of plant phospholipase D alpha”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.75). MolNFT v1 #155175 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KZ9
Type: protein
Length: 770 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase D alpha 1
EC: 3.1.4.4
UniProt: Q38882
Ligands: CA
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipase D alpha 1 (EC 3.1.4.4)	protein	770	25% helix, 27% strand	Q38882

Ligands and binding sites

CA · Calcium ion · metal · chains A

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

Pockets

9 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	82	0.75	0.98	24	empty
2	386	0.74	0.85	43	empty
3	111	0.50	0.81	21	empty
4	163	0.47	0.77	30	empty
5	146	0.44	0.75	29	empty

Compared structures

6KZ9 · Crystal structure of plant Phospholipase D alpha · the same entry in another collection · chain A against A, TM-score 1.00
Q38882 · AlphaFold monomer V2.0 prediction for phospholipase D alpha 1 (Q38882) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q38882
Elsewhere: RCSB PDB 6KZ9 · PDBe 6KZ9 · UniProt Q38882

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