Research workbench
Crystal structure of the post-catalytic product complex of polymerase lambda with an rcmp inserted opposite a templating G and damp inserted opposite a templating T at the primer terminus.
Analyse Crystal structure of the post-catalytic product complex of polymerase lambda… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UQ2
- Type
- protein + DNA
- Length
- 340 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
- PPV, MG, NA
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 318 | 49% helix, 15% 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)-R(P*CP*A)-3' | dna | 7 | — | — |
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A, P
- MG · Magnesium ion · metal · chains A, P
- NA · Sodium ion · metal · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.68 | 0.74 | 68 | PPV, MG |
| 2 | 134 | 0.55 | 0.82 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–T · 873 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–P · 573 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 384 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 325 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- T–D · 188 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 3UQ2 · Crystal structure of the post-catalytic product complex of polymerase lambda with an rCMP… · 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 3UQ2 · PDBe 3UQ2 · UniProt Q9UGP5
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