Research workbench
Crystal structure of an alka HOST/GUEST complex 8OXOGUANINE:CYTOSINE base pair
Analyse Crystal structure of an alka HOST/GUEST complex 8OXOGUANINE:CYTOSINE base pair in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CVT
- 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*(8OG)…
- EC
- 3.2.2.21
- UniProt
- P04395
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% 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 | 50% helix, 13% strand | P04395 |
| E, G | DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*(8OG) P*DAP*DGP*DTP*DGP*DCP*DC)-3') | dna | 12 | — | — |
| F, H | DNA (5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)- 3') | dna | 12 | — | — |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.85 | 0.85 | 102 | empty |
| 2 | 1193 | 0.83 | 0.84 | 118 | empty |
| 3 | 564 | 0.70 | 0.79 | 50 | empty |
| 4 | 208 | 0.65 | 0.84 | 24 | empty |
| 5 | 231 | 0.62 | 0.81 | 26 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1093 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1083 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 538 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- E–F · 519 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–E · 292 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3CVT · Crystal Structure of an AlkA Host/Guest Complex 8oxoGuanine: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 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 3CVT · PDBe 3CVT · UniProt P04395
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