Research workbench
Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a datp analog opposite a templating T and an rcmp at the primer terminus.
Analyse Crystal structure of the pre-catalytic ternary 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
- 4FO6
- Type
- protein + DNA
- Length
- 346 residues
- Chains
- 6
- 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
- F2A, NA, MG, MN, CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 315 | 48% helix, 16% 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*C)-3' | dna | 6 | — | — |
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| H | 5'-D(P*TP*AP*CP*TP*G)-3' | dna | 5 | — | — |
| I | 5'-D(P*CP*AP*GP*TP*A)-3' | dna | 5 | — | — |
Ligands and binding sites
- F2A · 2'-deoxy-5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]adenosine · ligand · chains A, T, P
- NA · Sodium ion · metal · 2 copies · chains A, D, P
- MG · Magnesium ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A, P
- CL · Chloride ion · ion · chains A, T
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 | 1031 | 0.68 | 0.74 | 76 | MG, F2A |
| 2 | 113 | 0.56 | 0.84 | 19 | empty |
| 3 | 133 | 0.39 | 0.74 | 19 | empty |
Interfaces
8 interfaces between chains.
- A–T · 832 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 380 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 374 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 280 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- A–H · 233 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4FO6 · Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP… · the same entry in another collection · chain P against P, 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 4FO6 · PDBe 4FO6 · UniProt Q9UGP5
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