MolNFT v1 · #81408 · protein + DNA
Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an ratp analog opposite a templating T.
3UPQ · DNA polymerase lambda: “Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an ratp analog opposite a…”. X-ray diffraction, 4 ligands (ZAN, MN, NA), 5 pockets (best druggability 0.68). MolNFT v1 #81408…
- PDB
- 3UPQ
- Type
- protein + DNA
- Length
- 329 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- ZAN, MN, NA, SO4
- Pockets
- 5 · best druggability 0.68
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 | 308 | 50% helix, 14% strand | Q9UGP5 |
| T | 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3' | dna | 11 | — | — |
| P | 5'-D(*CP*AP*GP*TP*AP*C)-3' | dna | 6 | — | — |
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
Ligands and binding sites
- ZAN · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- NA · Sodium ion · metal · chains A, P
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.68 | 0.75 | 51 | ZAN, MN |
| 2 | 78 | 0.62 | 0.90 | 20 | empty |
| 3 | 105 | 0.53 | 0.84 | 19 | empty |
| 4 | 92 | 0.49 | 0.82 | 21 | empty |
| 5 | 234 | 0.47 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–T · 767 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 385 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 370 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–P · 284 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- T–D · 190 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 3UPQ · Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP… · 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 0.99
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 Q9UGP5
- Elsewhere: RCSB PDB 3UPQ · PDBe 3UPQ · UniProt Q9UGP5
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