MolNFT v1 · #27399 · protein

Arginine residues as stabilizing elements in proteins

1XIM · D-xylose isomerase: “Arginine residues as stabilizing elements in proteins”. X-ray diffraction, 2 ligands (XYL, CO), 18 pockets (best druggability 0.84). MolNFT v1 #27399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XIM
Type: protein
Length: 1,568 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-xylose isomerase
EC: 5.3.1.5
UniProt: P12851
Ligands: XYL, CO
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-xylose isomerase (EC 5.3.1.5)	protein	392	50% helix, 10% strand	P12851

Ligands and binding sites

XYL · Xylitol · ligand · 4 copies · chains A, B, C, D
CO · Cobalt (II) ion · metal · 8 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	828	0.84	0.86	106	empty
2	794	0.83	0.86	99	empty
3	550	0.79	0.86	61	XYL
4	576	0.79	0.85	60	XYL
5	591	0.79	0.84	64	XYL, CO

Interfaces

6 interfaces between chains.

A–C · 5015 Å² buried · 84 hydrogen bonds · protein-protein
B–D · 5000 Å² buried · 86 hydrogen bonds · protein-protein
A–B · 1737 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1732 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1684 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

1XIM · Arginine residues as stabilizing elements in proteins · the same entry in another collection · chain A against A, TM-score 1.00
P12851 · AlphaFold monomer V2.0 prediction for xylose isomerase (P12851) · 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 P12851
Elsewhere: RCSB PDB 1XIM · PDBe 1XIM · UniProt P12851

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