Research workbench
Crystal structure analysis of the a-DNA decamer gcgt-2'OMEA-fat-acgc, with incorporated 2'-O-methylated-adenosine (2'OMEA) and 2'- fluoroarabino-thymidine (fat)
Analyse Crystal structure analysis of the a-DNA decamer gcgt-2'OMEA-fat-acgc, with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FIL
- Type
- DNA
- Length
- 40 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
- Ligands
- NCO
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.40 | 0.73 | 15 | NCO |
| 2 | 78 | 0.27 | 0.72 | 12 | NCO |
Interfaces
5 interfaces between chains.
- C–D · 474 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–B · 470 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–C · 112 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 101 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–D · 93 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 2FIL · Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-faT-ACGC, with Incorporated… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 2FIL · PDBe 2FIL
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