Research workbench
Human DNA ligase 1(E346A/E592A) bound to a bulged DNA substrate
Analyse Human DNA ligase 1(E346A/E592A) bound to a bulged DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KR3
- Type
- protein + DNA
- Length
- 669 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 1; DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3'); DNA…
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 1 (EC 6.5.1.1) | protein | 632 | 38% helix, 21% strand | P18858 |
| B | DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3') | dna | 12 | — | — |
| C | DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3') | dna | 7 | — | — |
| D | DNA (5'- D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.84 | 0.88 | 68 | AMP |
| 2 | 656 | 0.72 | 0.79 | 48 | empty |
| 3 | 390 | 0.68 | 0.81 | 39 | empty |
| 4 | 119 | 0.57 | 0.85 | 20 | ACT |
| 5 | 236 | 0.57 | 0.79 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1521 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–B · 713 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 609 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 497 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- C–D · 357 Ų buried · 31 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 7KR3 · PDBe 7KR3 · UniProt P18858
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