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Phospholipase A2, re-refinement of the pdb structure 1JQ8 without the putative complexed oligopeptide

Analyse Phospholipase A2, re-refinement of the pdb structure 1JQ8 without the putative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VET
Type: protein
Length: 242 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase A2 vrv-pl-viiia
EC: 3.1.1.4
UniProt: D0VX11
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4)	protein	121	48% helix, 8% strand	D0VX11

Pockets

4 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	247	0.76	0.89	33	empty
2	211	0.71	0.87	33	empty
3	158	0.57	0.81	23	empty
4	96	0.41	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 685 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

5VET · Phospholipase A2, re-refinement of the pdb structure 1JQ8 without the putative complexed… · the same entry in another collection · 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 D0VX11
Elsewhere: RCSB PDB 5VET · PDBe 5VET · UniProt D0VX11

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