Research workbench
Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating a and incorporated 8-oxo-dgmp
Analyse Crystal structure of the post-catalytic nick complex of DNA polymerase lambda… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X5V
- Type
- protein + DNA
- Length
- 339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(P*GP*CP*CP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- NA, MG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 317 | 50% helix, 14% strand | Q9UGP5 |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| P | DNA (5'-D(*CP*AP*GP*TP*AP*CP*(8OG))-3') | dna | 7 | — | — |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, P
- MG · Magnesium ion · metal · chains A, P
- CIT · Citric acid · additive · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.70 | 0.75 | 72 | NA, CIT |
| 2 | 150 | 0.60 | 0.84 | 35 | empty |
| 3 | 124 | 0.50 | 0.80 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–T · 947 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 565 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 410 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 321 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- D–T · 190 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4X5V · Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a… · the same entry in another collection · chain A against A, 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 4X5V · PDBe 4X5V · UniProt Q9UGP5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.