MolNFT v1 · #19215 · protein

Bacillus subtilis yabj

1QD9 · Purine regulatory protein yabj: “Bacillus subtilis yabj”. X-ray diffraction, 2 ligands (EMC, HG), 5 pockets (best druggability 0.79). MolNFT v1 #19215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QD9
Type: protein
Length: 372 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine regulatory protein yabj
UniProt: P37552
Ligands: EMC, HG
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Purine regulatory protein yabj	protein	124	31% helix, 31% strand	P37552

Ligands and binding sites

EMC · Ethyl mercury ion · ligand · 2 copies · chains B, C
HG · Mercury (II) ion · metal · chains A
ACY · Acetic acid · additive · 6 copies · chains A, C, B

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	109	0.79	0.98	27	empty
2	140	0.62	0.85	21	empty
3	178	0.61	0.83	22	empty
4	152	0.59	0.83	21	empty
5	88	0.56	0.86	15	empty

Interfaces

3 interfaces between chains.

B–C · 969 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 962 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 940 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1QD9 · Bacillus subtilis YABJ · the same entry in another collection · chain A against A, TM-score 1.00
P37552 · AlphaFold monomer V2.0 prediction for 2-IMINOBUTANOATE/2-iminopropanoate deaminase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P37552
Elsewhere: RCSB PDB 1QD9 · PDBe 1QD9 · UniProt P37552

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