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

Analyse Apo form of the Y31V mutant dimerization domain fragment of escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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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