MolNFT v1 · #152581 · protein + DNA
The crystal structure of ASFVLIG:CG complex
6IMK · DNA ligase: “The crystal structure of ASFVLIG:CG complex”. X-ray diffraction, 8 pockets (best druggability 0.81). MolNFT v1 #152581 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IMK
- Type
- protein + DNA
- Length
- 453 residues
- Chains
- 4
- 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
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase | protein | 409 | 23% helix, 34% strand | A0A0A1E0U0 |
| C | 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 | DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*G)-3') | dna | 12 | — | — |
| E | DNA (5'-D(P*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3') | dna | 10 | — | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.81 | 0.82 | 60 | empty |
| 2 | 87 | 0.74 | 0.96 | 21 | empty |
| 3 | 147 | 0.61 | 0.85 | 17 | empty |
| 4 | 143 | 0.47 | 0.78 | 16 | empty |
| 5 | 128 | 0.43 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1314 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–E · 717 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 624 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 565 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- C–E · 482 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 6IMK · The crystal structure of AsfvLIG:CG 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 6IMK · PDBe 6IMK · UniProt A0A0A1E0U0
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