Research workbench
Crystal structure of an alka HOST/GUEST complex N7METHYLGUANINE:CYTOSINE base pair
Analyse Crystal structure of an alka HOST/GUEST complex N7METHYLGUANINE:CYTOSINE base… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D4V
- Type
- protein + DNA
- Length
- 1,174 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-3-methyladenine glycosylase 2; 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC…
- EC
- 3.2.2.21
- UniProt
- P04395
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21) | protein | 282 | 47% helix, 12% strand | P04395 |
| C, D | DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21) | protein | 281 | 47% helix, 10% strand | P04395 |
| E, G | 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)- 3' | dna | 12 | — | — |
| F, H | 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3' | dna | 12 | — | — |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.85 | 0.85 | 115 | empty |
| 2 | 1058 | 0.84 | 0.85 | 120 | empty |
| 3 | 566 | 0.71 | 0.80 | 64 | empty |
| 4 | 562 | 0.66 | 0.76 | 43 | empty |
| 5 | 192 | 0.64 | 0.84 | 24 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1052 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1044 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 523 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- G–H · 521 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- B–F · 330 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3D4V · Crystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:Cytosine Base Pair · 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 C 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 3D4V · PDBe 3D4V · UniProt P04395
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