Research workbench
Human DNA ligase 1 bound to an adenylated, hydroxyl terminated DNA nick in edta
Analyse Human DNA ligase 1 bound to an adenylated, hydroxyl terminated DNA nick in edta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P0C
- Type
- protein + DNA
- Length
- 678 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, NA
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 1 (EC 6.5.1.1) | protein | 642 | 39% helix, 19% 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
- NA · Sodium ion · metal · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.84 | 0.85 | 84 | AMP, NA |
| 2 | 518 | 0.75 | 0.83 | 55 | empty |
| 3 | 507 | 0.67 | 0.79 | 44 | empty |
| 4 | 380 | 0.67 | 0.81 | 39 | empty |
| 5 | 188 | 0.60 | 0.82 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1564 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–C · 641 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 572 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 501 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- C–D · 353 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P0C · Human DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DNA nick in EDTA · the same entry in another collection · chain A against A, TM-score 1.00
- P18858 · AlphaFold monomer V2.0 prediction for DNA ligase 1 (P18858) · a predicted model of the same protein · 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 P18858
- Elsewhere: RCSB PDB 6P0C · PDBe 6P0C · UniProt P18858
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