MolNFT v1 · #62294 · protein

PLAP/P97 complex

3EBB · Phospholipase A2-activating protein: “PLAP/P97 complex”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.72). MolNFT v1 #62294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EBB
Type: protein
Length: 1,065 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase A2-activating protein; Transitional endoplasmic reticulum ATPase (ter ATP
UniProt: Q9Y263, P55072
Ligands: MG
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipase A2-activating protein	protein	265	70% helix, 0% strand	Q9Y263
B	Phospholipase A2-activating protein	protein	262	69% helix, 0% strand	Q9Y263
C	Phospholipase A2-activating protein	protein	265	71% helix, 0% strand	Q9Y263
D	Phospholipase A2-activating protein	protein	261	69% helix, 0% strand	Q9Y263
E	Transitional endoplasmic reticulum ATPase (ter ATP	protein	2	0% helix, 0% strand	P55072
F	Transitional endoplasmic reticulum ATPase (ter ATP	protein	4	0% helix, 0% strand	P55072
G	Transitional endoplasmic reticulum ATPase (ter ATP	protein	3	0% helix, 0% strand	P55072
H	Transitional endoplasmic reticulum ATPase (ter ATP	protein	3	0% helix, 0% strand	P55072

Ligands and binding sites

MG · Magnesium ion · metal · chains B

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.72	0.76	86	empty
2	407	0.65	0.78	43	empty
3	297	0.62	0.79	34	empty
4	365	0.60	0.77	38	empty
5	262	0.53	0.76	33	empty

Interfaces

9 interfaces between chains.

A–B · 1041 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1012 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 481 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 298 Å² buried · 1 hydrogen bond · protein-protein
D–H · 266 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

3EBB · PLAP/P97 complex · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y263 · AlphaFold monomer V2.0 prediction for phospholipase a-2-activating protein (Q9Y263) · 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 Q9Y263
Every structure of UniProt P55072
Elsewhere: RCSB PDB 3EBB · PDBe 3EBB · UniProt Q9Y263 · UniProt P55072

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