MolNFT v1 · #27859 · protein

K185N mutated S-adenosylhomocysteine hydrolase

1XWF · Adenosylhomocysteinase: “K185N mutated S-adenosylhomocysteine hydrolase”. X-ray diffraction, 2 ligands (NAD, ADN), 18 pockets (best druggability 0.89). MolNFT v1 #27859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XWF
Type: protein
Length: 1,720 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosylhomocysteinase
EC: 3.3.1.1
UniProt: P10760
Ligands: NAD, ADN
Pockets: 18 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	430	45% helix, 17% strand	P10760

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
ADN · Adenosine · ligand · 4 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.89	0.90	71	empty
2	906	0.84	0.86	90	NAD, ADN
3	1066	0.84	0.85	93	NAD, ADN
4	1020	0.83	0.84	89	NAD, ADN
5	1095	0.83	0.84	105	NAD, ADN

Interfaces

6 interfaces between chains.

C–D · 2968 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2916 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1670 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1667 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 467 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1XWF · K185N mutated S-adenosylhomocysteine hydrolase · the same entry in another collection · chain A against A, 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 0.97

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 1XWF · PDBe 1XWF · UniProt P10760

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