MolNFT v1 · #60611 · protein + DNA

Crystal structure of an alka HOST/GUEST complex 2'-fluoro-2'-deoxy-1, N6-ETHENOADENINE:THYMINE base pair

3CWU · DNA-3-methyladenine glycosylase 2: “Crystal structure of an alka HOST/GUEST complex 2'-fluoro-2'-deoxy-1, N6-ETHENOADENINE:THYMINE base pair”. X-ray diffraction, 13 pockets (best druggability 0.86). MolNFT v1 #60611 on GenesisL1: 3D…

PDB: 3CWU
Type: protein + DNA
Length: 1,176 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-3-methyladenine glycosylase 2; DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FE)…
EC: 3.2.2.21
UniProt: P04395
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21)	protein	282	49% helix, 11% strand	P04395
E, G	DNA (5'-D(DGPDAPDCPDAPDTPDGPDAP(2FE) PDTPDGPDCPDC)-3')	dna	12	—	—
F, H	DNA (5'-D(DGPDGPDCPDAPDTPDTPDCPDAPDTPDGPDTPDC)- 3')	dna	12	—	—

Pockets

13 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	1035	0.86	0.87	119	empty
2	1146	0.82	0.83	111	empty
3	671	0.68	0.77	49	empty
4	211	0.64	0.83	25	empty
5	523	0.63	0.76	35	empty

Interfaces

12 interfaces between chains.

A–D · 1105 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1038 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 518 Å² buried · 45 hydrogen bonds · nucleic-nucleic
E–F · 515 Å² buried · 49 hydrogen bonds · nucleic-nucleic
B–F · 301 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

3CWU · Crystal Structure of an AlkA Host/Guest Complex… · the same entry in another collection · chain H against H, TM-score 1.00
P04395 · AlphaFold monomer V2.0 prediction for DNA-3-methyladenine glycosylase 2 (P04395) · a predicted model of the same protein · chain B 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 P04395
Elsewhere: RCSB PDB 3CWU · PDBe 3CWU · UniProt P04395

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.