MolNFT v1 · #30095 · protein

E. COLI TRP repressor, tetragonal crystal form

1ZT9 · TRP operon repressor: “E. COLI TRP repressor, tetragonal crystal form”. X-ray diffraction, 2 ligands (TRP, SO4), 7 pockets (best druggability 0.64). MolNFT v1 #30095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZT9
Type: protein
Length: 404 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRP operon repressor
UniProt: P0A881
Ligands: TRP, SO4
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	TRP operon repressor	protein	101	81% helix, 0% strand	P0A881

Ligands and binding sites

TRP · Tryptophan · ligand · 4 copies · chains A, B, D, E
SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	569	0.64	0.75	43	empty
2	63	0.43	0.82	13	SO4, TRP
3	193	0.42	0.73	23	empty
4	68	0.40	0.80	12	SO4, TRP
5	92	0.39	0.77	18	TRP, SO4

Interfaces

4 interfaces between chains.

D–E · 2223 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2203 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 478 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 96 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1ZT9 · E. coli trp repressor, tetragonal crystal form · the same entry in another collection · chain E against E, TM-score 1.00
P0A881 · AlphaFold monomer V2.0 prediction for TRP operon repressor (P0A881) · 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 P0A881
Elsewhere: RCSB PDB 1ZT9 · PDBe 1ZT9 · UniProt P0A881

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