MolNFT v1 · #180547 · protein + DNA
Human DNA ligase 1 - R771W nicked DNA complex
7L35: “Human DNA ligase 1 - R771W nicked DNA complex”. X-ray diffraction, 2 ligands (AMP, NA), 6 pockets (best druggability 0.84). MolNFT v1 #180547 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7L35
- Type
- protein + DNA
- Length
- 670 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, NA
- Pockets
- 6 · best druggability 0.84
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 | 634 | 39% 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
- AMP · Adenosine monophosphate · ligand · chains A, C
- NA · Sodium ion · metal · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.84 | 0.85 | 84 | NA, AMP |
| 2 | 497 | 0.74 | 0.83 | 49 | empty |
| 3 | 370 | 0.71 | 0.83 | 45 | TRS |
| 4 | 279 | 0.70 | 0.85 | 32 | empty |
| 5 | 413 | 0.69 | 0.81 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1537 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–C · 611 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 607 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 503 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 359 Ų buried · 27 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 7L35 · PDBe 7L35 · UniProt P18858
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