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Argx from sulfolobus tokodaii complexed with LYSW/GLU/ADP/MG/ZN/SULFATE

Analyse Argx from sulfolobus tokodaii complexed with LYSW/GLU/ADP/MG/ZN/SULFATE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VPB
Type: protein
Length: 1,237 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative acetylornithine deacetylase; Alpha-aminoadipate carrier protein lysw
EC: 3.5.1.16
UniProt: Q970U6, Q976J8
Ligands: ADP, GLU, MG, ZN, SO4
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Putative acetylornithine deacetylase (EC 3.5.1.16)	protein	281	39% helix, 27% strand	Q970U6
B	Putative acetylornithine deacetylase (EC 3.5.1.16)	protein	282	39% helix, 27% strand	Q970U6
E, F	Alpha-aminoadipate carrier protein lysw	protein	56	0% helix, 45% strand	Q976J8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
GLU · Glutamic acid · ligand · 4 copies · chains A, E, B, F, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, E, F
SO4 · Sulfate ion · ion · 6 copies · chains A, E, B, F, C, D

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	795	0.86	0.89	114	ADP, GLU, MG, SO4
2	133	0.78	0.96	27	ADP, MG
3	140	0.78	0.95	27	ADP, MG
4	259	0.77	0.90	47	ADP, GLU, MG, SO4
5	59	0.73	0.99	21	empty

Interfaces

12 interfaces between chains.

C–D · 2047 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2044 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1151 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1136 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 962 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3VPB · ArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/Sulfate · the same entry in another collection · chain A against A, TM-score 1.00
Q970U6 · AlphaFold monomer V2.0 prediction for glutamate--lysw ligase argx (Q970U6) · a predicted model of the same protein · chain D against A, TM-score 0.99
Q976J8 · AlphaFold monomer V2.0 prediction for alpha-AMINOADIPATE/GLUTAMATE carrier protein lysw… · a predicted model of the same protein · chain F against A, TM-score 0.84

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 Q970U6
Every structure of UniProt Q976J8
Elsewhere: RCSB PDB 3VPB · PDBe 3VPB · UniProt Q970U6 · UniProt Q976J8

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