MolNFT v1 · #40600 · protein

Rmlc P aeruginosa with dtdp-rhamnose

2IXH · Dtdp-4-dehydrorhamnose 3,5-epimerase: “Rmlc P aeruginosa with dtdp-rhamnose”. X-ray diffraction, 1 ligand (TRH), 4 pockets (best druggability 0.58). MolNFT v1 #40600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2IXH
Type: protein
Length: 368 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dtdp-4-dehydrorhamnose 3,5-epimerase
UniProt: Q9HU21
Ligands: TRH
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dtdp-4-dehydrorhamnose 3,5-epimerase	protein	184	10% helix, 44% strand	Q9HU21

Ligands and binding sites

TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.58	0.81	33	TRH
2	212	0.57	0.80	35	TRH
3	50	0.45	0.84	17	empty
4	55	0.36	0.79	18	empty

Compared structures

2IXH · RmlC P aeruginosa with dTDP-rhamnose · the same entry in another collection · chain A against A, TM-score 1.00
Q9HU21 · AlphaFold monomer V2.0 prediction for dtdp-4-dehydrorhamnose 3,5-epimerase (Q9HU21) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9HU21
Elsewhere: RCSB PDB 2IXH · PDBe 2IXH · UniProt Q9HU21

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