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Earp bound with dtdp-rhamnose (soaked)

Analyse Earp bound with dtdp-rhamnose (soaked) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WXI
Type: protein
Length: 753 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Earp
UniProt: E6MVV9
Ligands: TRH, SO4
Pockets: 6 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Earp	protein	378	42% helix, 19% strand	E6MVV9
B	Earp	protein	375	42% helix, 18% strand	E6MVV9

Ligands and binding sites

TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	350	0.79	0.89	56	empty
2	276	0.78	0.90	44	TRH
3	243	0.78	0.91	36	TRH
4	99	0.52	0.83	16	empty
5	67	0.39	0.79	18	empty

Interfaces

1 interface between chains.

A–B · 1027 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (additive adduct).

Compared structures

5WXI · EarP bound with dTDP-rhamnose (soaked) · the same entry in another collection · chain A against A, 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 5WXI · PDBe 5WXI · UniProt E6MVV9

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