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A thermophilic hydrolase

Analyse A thermophilic hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X2E
Type: protein
Length: 1,604 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosylhomocysteinase
EC: 3.3.1.1
UniProt: O51933
Ligands: NAI
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	401	45% helix, 16% strand	O51933

Ligands and binding sites

NAI · 1,4-dihydronicotinamide 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

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.87	0.88	84	empty
2	934	0.78	0.80	88	NAI
3	899	0.77	0.80	88	NAI
4	800	0.76	0.80	76	NAI
5	1134	0.75	0.78	99	NAI

Interfaces

6 interfaces between chains.

C–D · 2239 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2223 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1787 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1722 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 401 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3X2E · A thermophilic hydrolase · the same entry in another collection · chain A against A, TM-score 1.00
O51933 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (O51933) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 O51933
Elsewhere: RCSB PDB 3X2E · PDBe 3X2E · UniProt O51933

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