MolNFT v1 · #159760 · protein + DNA
Human DNA ligase 1 bound to an adenylated, dideoxy terminated DNA nick with 2 mm MG2+
6P0A: “Human DNA ligase 1 bound to an adenylated, dideoxy terminated DNA nick with 2 mm MG2+”. X-ray diffraction, 2 ligands (AMP, MG), 8 pockets (best druggability 0.83). MolNFT v1 #159760 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6P0A
- Type
- protein + DNA
- Length
- 675 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 0.83
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 | 639 | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.83 | 0.88 | 77 | AMP |
| 2 | 414 | 0.75 | 0.85 | 43 | empty |
| 3 | 348 | 0.66 | 0.80 | 43 | empty |
| 4 | 283 | 0.62 | 0.80 | 32 | empty |
| 5 | 58 | 0.48 | 0.86 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1500 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–C · 554 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 524 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 504 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- C–D · 356 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P0A · Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 2 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 0.99
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 6P0A · PDBe 6P0A · UniProt P18858
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