Research workbench

Human givd cytosolic phospholipase A2

Analyse Human givd cytosolic phospholipase A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IZ5
Type: protein
Length: 1,503 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytosolic phospholipase A2 delta
EC: 3.1.1.4
UniProt: Q86XP0
Ligands: SO4
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Cytosolic phospholipase A2 delta (EC 3.1.1.4)	protein	746	27% helix, 27% strand	Q86XP0
A	Cytosolic phospholipase A2 delta (EC 3.1.1.4)	protein	757	30% helix, 27% strand	Q86XP0

Ligands and binding sites

SO4 · Sulfate ion · ion · 14 copies · chains B, A

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1073	0.79	0.80	95	empty
2	350	0.74	0.85	33	empty
3	242	0.57	0.79	26	empty
4	130	0.57	0.83	29	empty
5	212	0.55	0.79	35	SO4

Interfaces

1 interface between chains.

B–A · 1467 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5IZ5 · Human GIVD cytosolic phospholipase A2 · the same entry in another collection · chain B against B, TM-score 1.00
Q86XP0 · AlphaFold monomer V2.0 prediction for cytosolic phospholipase A2 delta (Q86XP0) · 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 Q86XP0
Elsewhere: RCSB PDB 5IZ5 · PDBe 5IZ5 · UniProt Q86XP0

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