MolNFT v1 · #187802 · protein + DNA
Crystal structure of ligase I with nick duplexes containing mismatch A:C
7SX5 · DNA ligase 1: “Crystal structure of ligase I with nick duplexes containing mismatch A:C”. X-ray diffraction, 1 ligand (AMP), 9 pockets (best druggability 0.84). MolNFT v1 #187802 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7SX5
- Type
- protein + DNA
- Length
- 673 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 1; DNA chain 1; DNA chain 2; DNA chain 3
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 1 (EC 6.5.1.1) | protein | 637 | 37% helix, 20% strand | P18858 |
| B | DNA chain 1 | dna | 11 | — | — |
| C | DNA chain 2 | dna | 7 | — | — |
| D | DNA chain 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.84 | 0.91 | 58 | AMP |
| 2 | 353 | 0.75 | 0.86 | 60 | empty |
| 3 | 494 | 0.73 | 0.82 | 39 | empty |
| 4 | 369 | 0.69 | 0.82 | 29 | empty |
| 5 | 224 | 0.50 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1329 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 603 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 570 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 505 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–D · 313 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 7SX5 · PDBe 7SX5 · UniProt P18858
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