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Fluoro-neplanocin a in human S-adenosylhomocysteine hydrolase

Analyse Fluoro-neplanocin a in human S-adenosylhomocysteine hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NJ4
Type: protein
Length: 1,722 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosylhomocysteinase
EC: 3.3.1.1
UniProt: P23526
Ligands: NAD, AFX
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Adenosylhomocysteinase (EC 3.3.1.1)	protein	431	44% helix, 16% strand	P23526
B, D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	430	44% helix, 16% strand	P23526

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
AFX · (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	741	0.88	0.91	72	empty
2	624	0.85	0.89	71	NAD, AFX
3	716	0.84	0.88	83	NAD, AFX
4	724	0.84	0.88	82	NAD, AFX
5	660	0.84	0.88	77	NAD, AFX

Interfaces

6 interfaces between chains.

C–D · 3270 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 3183 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 1895 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1893 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 464 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3NJ4 · Fluoro-neplanocin A in Human S-Adenosylhomocysteine Hydrolase · the same entry in another collection · chain A against A, TM-score 1.00
P23526 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P23526) · a predicted model of the same protein · chain B 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 P23526
Elsewhere: RCSB PDB 3NJ4 · PDBe 3NJ4 · UniProt P23526

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