MolNFT v1 · #152580 · protein + DNA
The crystal structure of se-ASFVLIG:DNA complex
6IMJ · DNA ligase: “The crystal structure of se-ASFVLIG:DNA complex”. X-ray diffraction, 3 ligands (ATP, CD, CL), 7 pockets (best druggability 0.81). MolNFT v1 #152580 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IMJ
- Type
- protein + DNA
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase; DNA (5'- D(*TP*C*CP*GP*GP*GP*AP*TP*GP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)…
- UniProt
- A0A0A1E0U0
- Ligands
- ATP, CD, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase | protein | 412 | 24% helix, 33% strand | A0A0A1E0U0 |
| B | DNA ligase | protein | 411 | 24% helix, 33% strand | A0A0A1E0U0 |
| C | DNA (5'- D(*TP*C*CP*GP*GP*GP*AP*TP*GP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)- 3') | dna | 19 | — | — |
| D | DNA (5'- D(*C*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)- 3') | dna | 21 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.81 | 0.86 | 95 | empty |
| 2 | 173 | 0.69 | 0.88 | 28 | empty |
| 3 | 180 | 0.64 | 0.85 | 24 | empty |
| 4 | 200 | 0.62 | 0.83 | 27 | ATP, CD |
| 5 | 227 | 0.61 | 0.81 | 27 | ATP, CD |
Interfaces
6 interfaces between chains.
- C–D · 895 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–C · 546 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 488 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 453 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 444 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified, 3 disulfide (engineered, disulfide).
Compared structures
- 6IMJ · The crystal structure of Se-AsfvLIG:DNA 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 6IMJ · PDBe 6IMJ · UniProt A0A0A1E0U0
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