MolNFT v1 · #169305 · protein

Crystal structure of the human nudix hydrolase NUDT16

6X7V · U8 snorna-decapping enzyme: “Crystal structure of the human nudix hydrolase NUDT16”. X-ray diffraction, 2 ligands (MN, CL), 8 pockets (best druggability 0.76). MolNFT v1 #169305 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6X7V
Type: protein
Length: 642 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U8 snorna-decapping enzyme
EC: 3.6.1.62, 3.6.1.64
UniProt: Q96DE0
Ligands: MN, CL
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64)	protein	157	30% helix, 32% strand	Q96DE0
B	U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64)	protein	158	29% helix, 33% strand	Q96DE0
C	U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64)	protein	159	30% helix, 32% strand	Q96DE0
D	U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64)	protein	168	29% helix, 32% strand	Q96DE0

Ligands and binding sites

MN · Manganese (II) ion · metal · chains A
CL · Chloride ion · ion · chains A, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	559	0.76	0.83	67	CL
2	69	0.73	0.98	22	empty
3	63	0.72	0.98	17	empty
4	146	0.47	0.77	27	empty
5	170	0.45	0.75	30	empty

Interfaces

5 interfaces between chains.

C–D · 1398 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1376 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 559 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 281 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 261 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6X7V · Crystal Structure of the Human Nudix Hydrolase Nudt16 · the same entry in another collection · chain D against D, TM-score 1.00
Q96DE0 · AlphaFold monomer V2.0 prediction for U8 snorna-decapping enzyme (Q96DE0) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q96DE0
Elsewhere: RCSB PDB 6X7V · PDBe 6X7V · UniProt Q96DE0

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