MolNFT v1 · #149900 · protein + DNA
DNA binding with a minimal scaffold: structure-function analysis of lig E DNA ligases
6GDR · DNA (5'- D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*…: “DNA binding with a minimal scaffold: structure-function analysis of lig E DNA ligases”. X-ray diffraction, 2 ligands (AMP, PO4), 4 pockets (best druggability 0.76).…
- PDB
- 6GDR
- Type
- protein + DNA
- Length
- 298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- 3'); DNA; DNA…
- UniProt
- A0A1J0SCU0
- Ligands
- AMP, PO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- 3') | dna | 21 | — | — |
| C | DNA | dna | 10 | — | — |
| D | DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3') | dna | 11 | — | — |
| A | DNA ligase | protein | 256 | 21% helix, 32% strand | A0A1J0SCU0 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains C, D, A
- PO4 · Phosphate ion · ion · 2 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.76 | 0.80 | 55 | PO4, AMP |
| 2 | 136 | 0.52 | 0.81 | 25 | empty |
| 3 | 141 | 0.48 | 0.78 | 16 | empty |
| 4 | 79 | 0.38 | 0.77 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–A · 923 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 533 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- D–A · 479 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 452 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- C–A · 359 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6GDR · DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases · the same entry in another collection · chain B against B, 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 A0A1J0SCU0
- Elsewhere: RCSB PDB 6GDR · PDBe 6GDR · UniProt A0A1J0SCU0
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