Research workbench

L-rhamnose isomerase

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

PDB: 1DE5
Type: protein
Length: 1,665 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-rhamnose isomerase
EC: 5.3.1.14
UniProt: P32170
Ligands: RNT, ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-rhamnose isomerase (EC 5.3.1.14)	protein	417	47% helix, 12% strand	P32170
B, C, D	L-rhamnose isomerase (EC 5.3.1.14)	protein	416	48% helix, 12% strand	P32170

Ligands and binding sites

RNT · L-rhamnitol · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.83	0.93	48	empty
2	288	0.81	0.93	56	empty
3	120	0.73	0.93	26	empty
4	818	0.73	0.78	110	empty
5	125	0.72	0.93	25	empty

Interfaces

6 interfaces between chains.

C–D · 2163 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2162 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 2080 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 2042 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 999 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1DE5 · L-rhamnose isomerase · the same entry in another collection · chain A against A, TM-score 1.00
P32170 · AlphaFold monomer V2.0 prediction for L-rhamnose isomerase (P32170) · a predicted model of the same protein · 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 P32170
Elsewhere: RCSB PDB 1DE5 · PDBe 1DE5 · UniProt P32170

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