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Hapalindole U and DMSPP Bound AmbP3

Analyse Hapalindole U and DMSPP Bound AmbP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y84
Type: protein
Length: 586 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Fischerella ambigua UTEX 1903
Molecule: AmbP3
UniProt: V5TDY7
Ligands: 8P6, DST
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · resolution 2 · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	AmbP3	protein	293	36% helix, 26% strand	V5TDY7

Ligands and binding sites

8P6 · Hapalindole U · ligand · 2 copies · chains A, B
DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B

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

Pockets

3 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	693	0.78	0.83	96	8P6, DST
2	502	0.77	0.85	66	8P6, DST
3	393	0.67	0.80	43	empty

Interfaces

1 interface between chains.

A–B · 411 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5Y84 · Hapalindole U and dmspp bound AMBP3 · the same entry in another collection · chain A against A, TM-score 1.00

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 V5TDY7
Elsewhere: RCSB PDB 5Y84 · PDBe 5Y84 · UniProt V5TDY7

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