MolNFT v1 · #143411 · protein

Crystal structure of campylobacter jejuni 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with hexylthio- dadme-immucillin-a

6AYS · 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase: “Crystal structure of campylobacter jejuni 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 1 ligand (HT6), 20 pockets (best…

PDB: 6AYS
Type: protein
Length: 1,832 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
EC: 3.2.2.9
UniProt: A0A1E7P7U4
Ligands: HT6
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9)	protein	229	38% helix, 30% strand	A0A1E7P7U4

Ligands and binding sites

HT6 · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(hexylsulfanyl)methyl]pyrrolidin-3-ol · ligand · 8 copies · chains A, B, C, G, D, H, E, F
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, F, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.87	0.90	118	EDO, HT6
2	351	0.80	0.90	49	HT6
3	276	0.79	0.91	39	HT6
4	831	0.77	0.80	70	empty
5	275	0.72	0.86	43	empty

Interfaces

17 interfaces between chains.

A–B · 1648 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1636 Å² buried · 18 hydrogen bonds · protein-protein
C–G · 1615 Å² buried · 17 hydrogen bonds · protein-protein
D–H · 1604 Å² buried · 18 hydrogen bonds · protein-protein
B–G · 468 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6AYS · Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine… · 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 A0A1E7P7U4
Elsewhere: RCSB PDB 6AYS · PDBe 6AYS · UniProt A0A1E7P7U4

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