Research workbench
Crystal structure of human DNA ligase I bound to 5'-adenylated, nicked DNA
Analyse Crystal structure of human DNA ligase I bound to 5'-adenylated, nicked DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X9N
- Type
- protein + DNA
- Length
- 672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dideoxy terminated DNA; 5'-phosphorylated DNA; Template DNA; DNA ligase I
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dideoxy terminated DNA | dna | 11 | — | — |
| C | 5'-phosphorylated DNA | dna | 9 | — | — |
| D | Template DNA | dna | 20 | — | — |
| A | DNA ligase I (EC 6.5.1.1) | protein | 632 | 39% helix, 21% strand | P18858 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.84 | 0.85 | 106 | AMP |
| 2 | 628 | 0.73 | 0.81 | 49 | empty |
| 3 | 307 | 0.69 | 0.84 | 30 | empty |
| 4 | 288 | 0.63 | 0.81 | 36 | empty |
| 5 | 303 | 0.62 | 0.80 | 26 | empty |
Interfaces
6 interfaces between chains.
- D–A · 1361 Ų buried · 44 hydrogen bonds · protein-nucleic
- C–A · 682 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 482 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- B–A · 478 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 440 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 7 modified, 1 covalent (engineered, covalent ligand, 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 P18858
- Elsewhere: RCSB PDB 1X9N · PDBe 1X9N · UniProt P18858
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