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Crystal structure of mycobacterium tuberculosis S-adenosyl-L- homocysteine hydrolase in ternary complex with NAD and 2- fluoroadenosine

Analyse Crystal structure of mycobacterium tuberculosis S-adenosyl-L- homocysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZJ0
Type: protein
Length: 1,941 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosylhomocysteinase
EC: 3.3.1.1
UniProt: P60176
Ligands: 2FA, NAD
Pockets: 17 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenosylhomocysteinase (EC 3.3.1.1)	protein	486	45% helix, 15% strand	P60176
B, C, D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	485	45% helix, 15% strand	P60176

Ligands and binding sites

2FA · 2-(6-amino-2-fluoro-purin-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · 4 copies · chains A, B, C, D
NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

17 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	601	0.87	0.92	61	empty
2	588	0.85	0.90	72	2FA, NAD
3	565	0.85	0.90	74	2FA, NAD
4	552	0.84	0.90	68	2FA, NAD
5	530	0.83	0.89	68	2FA, NAD

Interfaces

6 interfaces between chains.

C–D · 3371 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 3311 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 1835 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1805 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 527 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2ZJ0 · Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homocysteine hydrolase in… · 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 P60176
Elsewhere: RCSB PDB 2ZJ0 · PDBe 2ZJ0 · UniProt P60176

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