MolNFT v1 · #39553 · protein

Crystal structure of MN2+ bound ecai

2HXG · L-arabinose isomerase: “Crystal structure of MN2+ bound ecai”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.80). MolNFT v1 #39553 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2HXG
Type: protein
Length: 1,494 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-arabinose isomerase
EC: 5.3.1.4
UniProt: Q8FL89
Ligands: MN
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	L-arabinose isomerase (EC 5.3.1.4)	protein	498	40% helix, 21% strand	Q8FL89

Ligands and binding sites

MN · Manganese (II) ion · metal · 3 copies · chains A, B, C

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	502	0.80	0.87	54	empty
2	792	0.80	0.83	111	empty
3	498	0.79	0.86	56	empty
4	347	0.78	0.88	41	empty
5	78	0.71	0.95	18	empty

Interfaces

3 interfaces between chains.

B–C · 2403 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2399 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 2148 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

2HXG · Crystal Structure of Mn2+ bound ECAI · the same entry in another collection · chain A against A, TM-score 1.00
Q8FL89 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (Q8FL89) · a predicted model of the same protein · chain B 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 Q8FL89
Elsewhere: RCSB PDB 2HXG · PDBe 2HXG · UniProt Q8FL89

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