Research workbench

APO EARP

Analyse APO EARP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WXJ
Type: protein
Length: 746 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Earp
UniProt: E6MVV9
Ligands: SO4
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Earp	protein	374	43% helix, 19% strand	E6MVV9
B	Earp	protein	372	42% helix, 19% strand	E6MVV9

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, B
BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

7 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	1199	0.84	0.85	102	empty
2	213	0.63	0.83	25	SO4
3	175	0.61	0.83	26	SO4
4	114	0.55	0.84	15	empty
5	104	0.50	0.82	19	empty

Interfaces

1 interface between chains.

A–B · 1016 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (additive adduct).

Compared structures

5WXJ · Apo EarP · the same entry in another collection · chain B against B, TM-score 1.00
E6MVV9 · AlphaFold monomer V2.0 prediction for protein-arginine rhamnosyltransferase (E6MVV9) · 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 E6MVV9
Elsewhere: RCSB PDB 5WXJ · PDBe 5WXJ · UniProt E6MVV9

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