Research workbench
Human DNA ligase 1 bound to an adenylated, dideoxy terminated DNA nick with 200 mm MG2+
Analyse Human DNA ligase 1 bound to an adenylated, dideoxy terminated DNA nick with 200… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P09
- 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, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 1 (EC 6.5.1.1) | protein | 642 | 39% 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
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 85 | MG, AMP |
| 2 | 664 | 0.74 | 0.81 | 52 | MG |
| 3 | 430 | 0.68 | 0.81 | 43 | empty |
| 4 | 281 | 0.61 | 0.80 | 29 | empty |
| 5 | 175 | 0.59 | 0.83 | 28 | MG |
Interfaces
6 interfaces between chains.
- A–D · 1555 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–C · 603 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 543 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 504 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 355 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P09 · Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+ · 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 6P09 · PDBe 6P09 · UniProt P18858
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