Research workbench
Human DNA ligase 1 - R641L nicked DNA complex
Analyse Human DNA ligase 1 - R641L nicked DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L34
- Type
- protein + DNA
- Length
- 673 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 1; DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'); DNA…
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 1 (EC 6.5.1.1) | protein | 637 | 38% helix, 20% strand | P18858 |
| B | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') | dna | 7 | — | — |
| D | DNA (5'- D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.83 | 0.88 | 77 | AMP |
| 2 | 1145 | 0.77 | 0.80 | 99 | empty |
| 3 | 512 | 0.66 | 0.78 | 47 | empty |
| 4 | 78 | 0.53 | 0.86 | 19 | empty |
| 5 | 51 | 0.42 | 0.84 | 9 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1337 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–C · 610 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 508 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–B · 484 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–D · 359 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 7L34 · PDBe 7L34 · UniProt P18858
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