MolNFT v1 · #143410 · protein

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

6AYR · 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase: “Crystal structure of campylobacter jejuni 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 1 ligand (BIG), 8 pockets (best…

PDB: 6AYR
Type: protein
Length: 916 residues
Chains: 4
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: BIG
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9)	protein	229	38% helix, 29% strand	A0A1E7P7U4

Ligands and binding sites

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

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.83	0.84	130	BIG
2	123	0.74	0.93	24	BIG
3	129	0.73	0.92	24	BIG
4	134	0.72	0.92	28	BIG
5	80	0.58	0.88	28	empty

Interfaces

6 interfaces between chains.

C–D · 1607 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1607 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 274 Å² buried · 1 hydrogen bond · protein-protein
B–C · 43 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 29 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6AYR · 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 6AYR · PDBe 6AYR · UniProt A0A1E7P7U4

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