MolNFT v1 · #148119 · protein

NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii complexed with adenosine

6EXI · Adenosylhomocysteinase: “NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii complexed with…”. X-ray diffraction, 2 ligands (ADN, NA), 18 pockets (best druggability 0.89). MolNFT v1 #148119…

PDB: 6EXI
Type: protein
Length: 1,874 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosylhomocysteinase
EC: 3.3.1.1
UniProt: A0A087WNH6
Ligands: ADN, NA
Pockets: 18 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	468	46% helix, 14% strand	A0A087WNH6
B	Adenosylhomocysteinase (EC 3.3.1.1)	protein	470	46% helix, 14% strand	A0A087WNH6

Ligands and binding sites

ADN · Adenosine · ligand · 8 copies · chains A, B, C, D
NA · Sodium ion · metal · 4 copies · chains A, C, B, D
PEG · Di(hydroxyethyl)ether · additive · chains C

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

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1010	0.89	0.91	93	empty
2	1082	0.84	0.85	113	ADN
3	1165	0.84	0.85	113	ADN
4	1185	0.83	0.84	120	ADN
5	737	0.83	0.86	72	ADN

Interfaces

6 interfaces between chains.

A–B · 3061 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 3060 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 1778 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 1776 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 417 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6EXI · NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium… · 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 A0A087WNH6
Elsewhere: RCSB PDB 6EXI · PDBe 6EXI · UniProt A0A087WNH6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.