Research workbench

Rat liver S-adenosylhomocystein hydrolase

Analyse Rat liver S-adenosylhomocystein hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1B3R
Type: protein
Length: 1,712 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (S-adenosylhomocysteine hydrolase)
EC: 3.3.1.1
UniProt: P10760
Ligands: NAD
Pockets: 15 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein (S-adenosylhomocysteine hydrolase) (EC 3.3.1.1)	protein	428	43% helix, 18% strand	P10760

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, 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	1186	0.88	0.89	75	empty
2	1179	0.82	0.83	115	NAD
3	1192	0.82	0.83	116	NAD
4	1107	0.82	0.83	110	NAD
5	1117	0.82	0.83	112	NAD

Interfaces

6 interfaces between chains.

A–B · 2958 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 2936 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 1524 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1514 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 483 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1B3R · Rat liver S-adenosylhomocystein hydrolase · the same entry in another collection · chain B against B, TM-score 1.00
P10760 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P10760) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 P10760
Elsewhere: RCSB PDB 1B3R · PDBe 1B3R · UniProt P10760

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