MolNFT v1 · #115326 · protein + DNA

NGTET1 in complex with 5MC DNA in space group P3221

5CG9 · Tet-like dioxygenase: “NGTET1 in complex with 5MC DNA in space group P3221”. X-ray diffraction, 3 ligands (AKG, MN, SO4), 10 pockets (best druggability 0.75). MolNFT v1 #115326 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5CG9
Type: protein + DNA
Length: 578 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tet-like dioxygenase; DNA (5'-D(P*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'); DNA…
UniProt: D2W6T1
Ligands: AKG, MN, SO4
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tet-like dioxygenase	protein	267	34% helix, 25% strand	D2W6T1
B, E	DNA (5'-D(PCPAPTPGPCPGPCPTPGPAP*C)-3')	dna	11	—	—
C	DNA (5'-D(TPGPTPCPAPGP(5CM)PGPCPAPTPGP*G)-3')	dna	12	—	—
D	Tet-like dioxygenase	protein	264	33% helix, 27% strand	D2W6T1
F	DNA (5'-D(TPGPTPCPAPGP(5CM)PGPCPAPTPGP*G)-3')	dna	13	—	—

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, C, D, F
MN · Manganese (II) ion · metal · 2 copies · chains A, D
SO4 · Sulfate ion · ion · 3 copies · chains A, D
EDO · 1,2-ethanediol · additive · 2 copies · chains A, D, E, F

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.75	0.99	21	AKG, MN
2	62	0.72	0.98	21	AKG, MN
3	298	0.65	0.82	30	empty
4	397	0.64	0.79	38	empty
5	169	0.55	0.80	37	SO4, EDO

Interfaces

7 interfaces between chains.

A–D · 982 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 555 Å² buried · 14 hydrogen bonds · protein-nucleic
D–F · 553 Å² buried · 14 hydrogen bonds · protein-nucleic
E–F · 530 Å² buried · 46 hydrogen bonds · nucleic-nucleic
B–C · 499 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5CG9 · NgTET1 in complex with 5mC DNA in space group P3221 · the same entry in another collection · chain F against F, 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 5CG9 · PDBe 5CG9 · UniProt D2W6T1

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