Research workbench
Oxog-modified insertion ternary complex
Analyse Oxog-modified insertion ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ASD
- Type
- protein + DNA
- Length
- 744 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'; 5'-D(*CP*T*AP*AP*CP*(8OG)…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DCP, CA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, H | 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3' | dna | 13 | — | — |
| E | 5'-D(*CP*T*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' | dna | 17 | — | — |
| J | 5'-D(*CP*T*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' | dna | 19 | — | — |
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 25% strand | Q97W02 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains D, E, A, H, J, B
- CA · Calcium ion · metal · 7 copies · chains D, A, H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.80 | 0.81 | 69 | CA, DCP |
| 2 | 980 | 0.78 | 0.80 | 60 | empty |
| 3 | 624 | 0.74 | 0.81 | 46 | empty |
| 4 | 705 | 0.73 | 0.80 | 43 | empty |
| 5 | 295 | 0.59 | 0.78 | 33 | CA, DCP |
Interfaces
8 interfaces between chains.
- J–B · 1092 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–A · 1092 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–A · 634 Ų buried · 15 hydrogen bonds · protein-nucleic
- H–B · 628 Ų buried · 13 hydrogen bonds · protein-nucleic
- H–J · 612 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
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 Q97W02
- Elsewhere: RCSB PDB 2ASD · PDBe 2ASD · UniProt Q97W02
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