MolNFT v1 · #115325 · protein + DNA

NGTET1 in complex with 5HMC DNA

5CG8 · Tet-like dioxygenase: “NGTET1 in complex with 5HMC DNA”. X-ray diffraction, 2 ligands (AKG, MN), 3 pockets (best druggability 0.72). MolNFT v1 #115325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CG8
Type: protein + DNA
Length: 294 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tet-like dioxygenase; DNA (5'-D(*AP*GP*AP*AP*TP*TP*CP*CP*GP*TP*TP*CP*CP*A)-3'); DNA…
UniProt: D2W6T1
Ligands: AKG, MN
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tet-like dioxygenase	protein	266	32% helix, 26% strand	D2W6T1
B	DNA (5'-D(APGPAPAPTPTPCPCPGPTPTPCPCPA)-3')	dna	14	—	—
C	DNA (5'-D(TPGPGPAPAP(5HC)PGPGPAPAPTPTPCPT)- 3')	dna	14	—	—

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · chains A, C
MN · Manganese (II) ion · metal · chains A, C

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.72	0.99	20	AKG
2	396	0.65	0.79	42	empty
3	90	0.43	0.79	14	empty

Interfaces

3 interfaces between chains.

B–C · 600 Å² buried · 52 hydrogen bonds · nucleic-nucleic
A–C · 597 Å² buried · 13 hydrogen bonds · protein-nucleic
A–B · 325 Å² buried · 3 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5CG8 · NgTET1 in complex with 5hmC DNA · the same entry in another collection · chain A against A, TM-score 1.00
D2W6T1 · AlphaFold monomer V2.0 prediction for tet-like dioxygenase 1 (D2W6T1) · a predicted model of the same protein · 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 D2W6T1
Elsewhere: RCSB PDB 5CG8 · PDBe 5CG8 · UniProt D2W6T1

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