Research workbench
Crystal structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate
Analyse Crystal structure of human DNA polymerase lambda in complex with nicked DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XSP
- Type
- protein + DNA
- Length
- 349 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3'; 5'-D(*CP*AP*GP*TP*AP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- PPV, NA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3' | dna | 11 | — | — |
| P | 5'-D(*CP*AP*GP*TP*AP*CP*G)-3' | dna | 7 | — | — |
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 327 | 47% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.66 | 0.77 | 40 | NA, PPV |
| 2 | 108 | 0.55 | 0.84 | 31 | empty |
| 3 | 136 | 0.52 | 0.81 | 23 | empty |
| 4 | 174 | 0.47 | 0.76 | 21 | empty |
Interfaces
5 interfaces between chains.
- T–A · 943 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–A · 590 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–A · 393 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–P · 327 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- T–D · 186 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Compared structures
- 1XSP · Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and… · the same entry in another collection · chain T against T, TM-score 1.00
- Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9UGP5
- Elsewhere: RCSB PDB 1XSP · PDBe 1XSP · UniProt Q9UGP5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.