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Structure of chlorella virus DNA ligase-product DNA complex
Analyse Structure of chlorella virus DNA ligase-product DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q2U
- Type
- protein + DNA
- Length
- 1,340 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP *AP*AP*T)-3'…
- UniProt
- O41026
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G, I, K | 5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP *AP*AP*T)-3' | dna | 21 | — | — |
| F, H, J, L | 5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC) P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3' | dna | 21 | — | — |
| A, B, C, D | Chlorella virus DNA ligase | protein | 293 | 24% helix, 35% strand | O41026 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.85 | 0.86 | 64 | empty |
| 2 | 1037 | 0.84 | 0.85 | 73 | empty |
| 3 | 1040 | 0.84 | 0.85 | 71 | empty |
| 4 | 1005 | 0.84 | 0.85 | 71 | empty |
| 5 | 438 | 0.65 | 0.78 | 25 | empty |
Interfaces
17 interfaces between chains.
- I–C · 1051 Ų buried · 18 hydrogen bonds · protein-nucleic
- K–D · 1048 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–A · 1047 Ų buried · 19 hydrogen bonds · protein-nucleic
- G–B · 1044 Ų buried · 18 hydrogen bonds · protein-nucleic
- H–B · 983 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2Q2U · Structure of Chlorella virus DNA ligase-product DNA complex · the same entry in another collection · chain E against E, 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
- Every structure of UniProt O41026
- Elsewhere: RCSB PDB 2Q2U · PDBe 2Q2U · UniProt O41026
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