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Crystal structure of a T.THERMOPHILUS HB8 AP6A hydrolase NDX1-AP6A complex

Analyse Crystal structure of a T.THERMOPHILUS HB8 AP6A hydrolase NDX1-AP6A complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VC8
Type: protein
Length: 252 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NDX1
UniProt: Q75UV1
Ligands: 5FA
Pockets: 2 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NDX1	protein	126	26% helix, 40% strand	Q75UV1

Ligands and binding sites

5FA · Adenosine-5'-pentaphosphate · ligand · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	232	0.53	0.76	29	5FA
2	219	0.53	0.77	28	5FA

Interfaces

1 interface between chains.

A–B · 616 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1VC8 · Crystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex · the same entry in another collection · chain A against A, TM-score 1.00
Q75UV1 · AlphaFold monomer V2.0 prediction for diadenosine hexaphosphate hydrolase (Q75UV1) · 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 Q75UV1
Elsewhere: RCSB PDB 1VC8 · PDBe 1VC8 · UniProt Q75UV1

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