MolNFT v1 · #24852 · protein

Crystal structure of a hydrolase

1V8B · Adenosylhomocysteinase: “Crystal structure of a hydrolase”. X-ray diffraction, 2 ligands (NAD, ADN), 14 pockets (best druggability 0.89). MolNFT v1 #24852 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1V8B
Type: protein
Length: 1,904 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosylhomocysteinase
EC: 3.3.1.1
UniProt: P50250
Ligands: NAD, ADN
Pockets: 14 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Adenosylhomocysteinase (EC 3.3.1.1)	protein	476	45% helix, 14% strand	P50250

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
ADN · Adenosine · ligand · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1073	0.89	0.91	73	empty
2	709	0.87	0.90	90	NAD, ADN
3	983	0.87	0.88	111	NAD, ADN
4	848	0.86	0.88	93	NAD, ADN
5	960	0.86	0.87	116	NAD, ADN

Interfaces

6 interfaces between chains.

C–D · 3144 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 3092 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 2087 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 2066 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 526 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1V8B · Crystal structure of a hydrolase · the same entry in another collection · chain A against A, TM-score 1.00
P50250 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P50250) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P50250
Elsewhere: RCSB PDB 1V8B · PDBe 1V8B · UniProt P50250

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