Research workbench
Crystal structure of ligase I with nick duplexes containing cognate G:T
Analyse Crystal structure of ligase I with nick duplexes containing cognate G:T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SXE
- Type
- protein + DNA
- Length
- 674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 1; DNA chain 1; DNA chain 2; DNA chain 3
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 1 (EC 6.5.1.1) | protein | 638 | 37% helix, 18% strand | P18858 |
| B | DNA chain 1 | dna | 11 | — | — |
| C | DNA chain 2 | dna | 7 | — | — |
| D | DNA chain 3 | dna | 18 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, B, C
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 | 1068 | 0.84 | 0.85 | 124 | AMP |
| 2 | 377 | 0.69 | 0.82 | 37 | empty |
| 3 | 256 | 0.58 | 0.79 | 24 | empty |
| 4 | 89 | 0.52 | 0.83 | 23 | empty |
| 5 | 182 | 0.51 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1367 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 557 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 551 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 521 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- C–D · 342 Ų buried · 29 hydrogen bonds · nucleic-nucleic
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 7SXE · PDBe 7SXE · UniProt P18858
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