MolNFT v1 · #59981 · protein

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

3CE6 · Adenosylhomocysteinase: “Crystal structure of mycobacterium tuberculosis S-adenosyl-L- homocysteine hydrolase in ternary complex with…”. X-ray diffraction, 2 ligands (ADN, NAD), 18 pockets (best druggability 0.86). MolNFT v1 #59981…

PDB: 3CE6
Type: protein
Length: 1,940 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: ADN, NAD
Pockets: 18 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenosylhomocysteinase (EC 3.3.1.1)	protein	486	48% helix, 14% strand	P60176
B, C	Adenosylhomocysteinase (EC 3.3.1.1)	protein	485	47% helix, 14% strand	P60176
D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	484	47% helix, 15% strand	P60176

Ligands and binding sites

ADN · Adenosine · 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

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	928	0.86	0.88	109	empty
2	537	0.85	0.91	72	ADN, NAD
3	550	0.85	0.90	71	ADN, NAD
4	559	0.84	0.90	71	ADN, NAD
5	561	0.84	0.89	74	ADN, NAD

Interfaces

6 interfaces between chains.

C–D · 3344 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 3333 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 1802 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1800 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 524 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3CE6 · 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 3CE6 · PDBe 3CE6 · UniProt P60176

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