MolNFT v1 · #180167 · protein + DNA
Human DNA ligase 1(E346A/E592A) bound to a nicked DNA substrate control duplex
7KR4: “Human DNA ligase 1(E346A/E592A) bound to a nicked DNA substrate control duplex”. X-ray diffraction, 1 ligand (AMP), 6 pockets (best druggability 0.83). MolNFT v1 #180167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KR4
- 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(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*C)-3'); DNA…
- EC
- 6.5.1.1
- UniProt
- P18858
- Ligands
- AMP
- Pockets
- 6 · best druggability 0.83
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 | 639 | 39% helix, 20% strand | P18858 |
| B | DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3') | dna | 7 | — | — |
| D | DNA (5'- D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.83 | 0.88 | 82 | AMP |
| 2 | 404 | 0.67 | 0.81 | 41 | empty |
| 3 | 204 | 0.66 | 0.86 | 30 | empty |
| 4 | 184 | 0.62 | 0.83 | 26 | empty |
| 5 | 267 | 0.56 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1483 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–C · 618 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 549 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 486 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- C–D · 347 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7KR4 · Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex · 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 7KR4 · PDBe 7KR4 · UniProt P18858
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