Research workbench
The crystal structure of ASFVLIG:CT2 complex
Analyse The crystal structure of ASFVLIG:CT2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IMN
- Type
- protein + DNA
- Length
- 907 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase; DNA (5'- D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)…
- UniProt
- A0A0A1E0U0
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase | protein | 411 | 20% helix, 33% strand | A0A0A1E0U0 |
| B | DNA ligase | protein | 408 | 20% helix, 33% strand | A0A0A1E0U0 |
| C, F | DNA (5'- D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)- 3') | dna | 22 | — | — |
| D, G | DNA (5'- D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)- 3') | dna | 22 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.83 | 0.84 | 71 | empty |
| 2 | 1132 | 0.82 | 0.84 | 77 | empty |
| 3 | 61 | 0.70 | 0.97 | 24 | empty |
| 4 | 585 | 0.69 | 0.78 | 61 | empty |
| 5 | 56 | 0.68 | 0.97 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–G · 1303 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–F · 1263 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 1231 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–C · 1206 Ų buried · 23 hydrogen bonds · protein-nucleic
- F–G · 1006 Ų buried · 101 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6IMN · The crystal structure of AsfvLIG:CT2 complex · 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
- Every structure of UniProt A0A0A1E0U0
- Elsewhere: RCSB PDB 6IMN · PDBe 6IMN · UniProt A0A0A1E0U0
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