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Crystal structure of the E. COLI glyoxylate regulatory protein ligand binding domain

Analyse Crystal structure of the E. COLI glyoxylate regulatory protein ligand binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TF1
Type: protein
Length: 724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Negative regulator of allantoin and glyoxylate utilization operons
UniProt: P0ACN4
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Negative regulator of allantoin and glyoxylate utilization operons	protein	184	41% helix, 24% strand	P0ACN4
B	Negative regulator of allantoin and glyoxylate utilization operons	protein	178	44% helix, 25% strand	P0ACN4
C	Negative regulator of allantoin and glyoxylate utilization operons	protein	179	44% helix, 23% strand	P0ACN4
D	Negative regulator of allantoin and glyoxylate utilization operons	protein	183	41% helix, 22% strand	P0ACN4

Pockets

7 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	839	0.75	0.79	115	empty
2	218	0.60	0.81	32	empty
3	100	0.57	0.86	25	empty
4	171	0.49	0.77	30	empty
5	111	0.43	0.77	19	empty

Interfaces

4 interfaces between chains.

C–D · 780 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 661 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 425 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 423 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1TF1 · Crystal Structure of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain · the same entry in another collection · chain D against D, TM-score 1.00
P0ACN4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor allr (P0ACN4) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P0ACN4
Elsewhere: RCSB PDB 1TF1 · PDBe 1TF1 · UniProt P0ACN4

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