MolNFT v1 · #109931 · protein

Rhamnosidase from klebsiella oxytoca with rhamnose bound

4XHC · Alpha-L-rhamnosidase: “Rhamnosidase from klebsiella oxytoca with rhamnose bound”. X-ray diffraction, 2 ligands (RAM, SO4), 13 pockets (best druggability 0.70). MolNFT v1 #109931 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4XHC
Type: protein
Length: 1,026 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-L-rhamnosidase
EC: 3.2.1.40
UniProt: G8WCL1
Ligands: RAM, SO4
Pockets: 13 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-L-rhamnosidase (EC 3.2.1.40)	protein	513	41% helix, 22% strand	G8WCL1

Ligands and binding sites

RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	514	0.70	0.80	59	empty
2	250	0.69	0.85	34	empty
3	179	0.66	0.85	27	RAM
4	183	0.66	0.85	27	RAM
5	202	0.57	0.80	36	empty

Interfaces

1 interface between chains.

A–B · 1432 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4XHC · rhamnosidase from Klebsiella oxytoca with rhamnose bound · 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 G8WCL1
Elsewhere: RCSB PDB 4XHC · PDBe 4XHC · UniProt G8WCL1

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