MolNFT v1 · #32342 · protein

Pli mutant E20C L16G Y17H, antiparallel

2BNI · General control protein GCN4: “Pli mutant E20C L16G Y17H, antiparallel”. X-ray diffraction, 1 ligand (TYZ), 2 pockets (best druggability 0.80). MolNFT v1 #32342 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BNI
Type: protein
Length: 126 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: General control protein GCN4
UniProt: P03069
Ligands: TYZ
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 92% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	General control protein GCN4	protein	29	93% helix, 0% strand	P03069
B, C	General control protein GCN4	protein	33	94% helix, 0% strand	P03069
D	General control protein GCN4	protein	31	90% helix, 0% strand	P03069

Ligands and binding sites

TYZ · Para acetamido benzoic acid · ligand · 2 copies · chains B, C

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

Pockets

2 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	135	0.80	0.97	24	empty
2	53	0.30	0.75	14	empty

Interfaces

6 interfaces between chains.

B–D · 763 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 735 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 734 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 583 Å² buried · 1 hydrogen bond · protein-protein
C–D · 122 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

2BNI · pLI mutant E20C L16G Y17H, antiparallel · the same entry in another collection · chain D against D, TM-score 1.00
P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P03069
Elsewhere: RCSB PDB 2BNI · PDBe 2BNI · UniProt P03069

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