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Aeromonas hydrophila mtan-2 complexed with adenine

Analyse Aeromonas hydrophila mtan-2 complexed with adenine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K2Q
Type: protein
Length: 910 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: A0KIZ1
Ligands: ADE
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9)	protein	227	37% helix, 33% strand	A0KIZ1
B, D	5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9)	protein	228	36% helix, 32% strand	A0KIZ1

Ligands and binding sites

ADE · Adenine · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 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	1199	0.79	0.81	98	empty
2	67	0.74	0.98	22	ADE
3	61	0.73	0.99	20	ADE
4	129	0.69	0.90	24	ADE
5	120	0.69	0.90	26	ADE

Interfaces

5 interfaces between chains.

C–D · 1649 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1603 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 694 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 202 Å² buried · 1 hydrogen bond · protein-protein
A–C · 200 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6K2Q · Aeromonas hydrophila MtaN-2 complexed with adenine · the same entry in another collection · chain A against A, TM-score 1.00
A0KIZ1 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · 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 A0KIZ1
Elsewhere: RCSB PDB 6K2Q · PDBe 6K2Q · UniProt A0KIZ1

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