MolNFT v1 · #187755 · protein + DNA
Crystal structure of human ligase I with nick duplexes containing cognate A:T
7SUM · DNA ligase 1: “Crystal structure of human ligase I with nick duplexes containing cognate A:T”. X-ray diffraction, 1 ligand (AMP), 11 pockets (best druggability 0.83). MolNFT v1 #187755 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7SUM
- Type
- protein + DNA
- Length
- 681 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 1; DNA(5'-*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*A-3')…
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 11 · 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 | 645 | 38% helix, 20% strand | P18858 |
| B | DNA(5'-*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*A-3') | dna | 11 | — | — |
| C | DNA(5'-P*GP*TP*CP*GP*GP*AP*C-3') | dna | 7 | — | — |
| D | DNA(5'- *GP*TP*CP*CP*GP*AP*CP*TP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C-3') | dna | 18 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.83 | 0.84 | 102 | AMP |
| 2 | 310 | 0.71 | 0.85 | 32 | empty |
| 3 | 285 | 0.68 | 0.84 | 47 | empty |
| 4 | 265 | 0.62 | 0.81 | 31 | empty |
| 5 | 72 | 0.54 | 0.87 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1466 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–C · 581 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 525 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 506 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- C–D · 338 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7SUM · Crystal structure of human ligase I with nick duplexes containing cognate A:T · 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 7SUM · PDBe 7SUM · UniProt P18858
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