MolNFT v1 · #27420 · protein

Apo form of the Y31V mutant dimerization domain fragment of escherichia COLI regulatory protein arac

1XJA · Arabinose operon regulatory protein: “Apo form of the Y31V mutant dimerization domain fragment of escherichia COLI regulatory protein arac”. X-ray diffraction, 10 pockets (best druggability 0.73). MolNFT v1 #27420 on GenesisL1: 3D…

PDB: 1XJA
Type: protein
Length: 816 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arabinose operon regulatory protein
UniProt: P0A9E0
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 26% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arabinose operon regulatory protein	protein	165	26% helix, 35% strand	P0A9E0
B	Arabinose operon regulatory protein	protein	154	27% helix, 37% strand	P0A9E0
C	Arabinose operon regulatory protein	protein	169	26% helix, 34% strand	P0A9E0
D	Arabinose operon regulatory protein	protein	165	26% helix, 34% strand	P0A9E0
E	Arabinose operon regulatory protein	protein	163	26% helix, 33% strand	P0A9E0

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, C, D, E

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.73	0.83	41	EDO
2	311	0.67	0.82	39	EDO
3	217	0.57	0.79	23	EDO
4	137	0.49	0.79	21	empty
5	78	0.46	0.81	17	EDO

Interfaces

4 interfaces between chains.

C–D · 913 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 815 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 609 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 490 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1XJA · Apo form of the Y31V mutant dimerization domain fragment of Escherichia coli regulatory… · the same entry in another collection · chain E against E, TM-score 1.00
P0A9E0 · AlphaFold monomer V2.0 prediction for arabinose operon regulatory protein (P0A9E0) · a predicted model of the same protein · chain B 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 P0A9E0
Elsewhere: RCSB PDB 1XJA · PDBe 1XJA · UniProt P0A9E0

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