Research workbench
Crystal structure of a polymerase lambda variant with a dgtp analog opposite a templating T
Analyse Crystal structure of a polymerase lambda variant with a dgtp analog opposite a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PML
- Type
- protein + DNA
- Length
- 688 residues
- Chains
- 8
- 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'; 5'-D(P*GP*CP*CP*G)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- 1GC, MG, NA
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 322 | 48% helix, 14% strand | Q9UGP5 |
| B | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 48% helix, 15% strand | Q9UGP5 |
| C, E | 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3' | dna | 11 | — | — |
| D, G | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| F, H | 5'-D(*CP*AP*GP*TP*AP*C)-3' | dna | 6 | — | — |
Ligands and binding sites
- 1GC · 2'-deoxy-5'-O-[(R)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]guanosine · ligand · 2 copies · chains A, C, H, B, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, H, B, F
- NA · Sodium ion · metal · 3 copies · chains A, H, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.79 | 0.81 | 107 | empty |
| 2 | 834 | 0.71 | 0.77 | 58 | 1GC, MG, NA |
| 3 | 1141 | 0.71 | 0.75 | 67 | 1GC, MG, NA |
| 4 | 124 | 0.54 | 0.83 | 22 | empty |
| 5 | 298 | 0.53 | 0.75 | 32 | empty |
Interfaces
15 interfaces between chains.
- A–C · 717 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–E · 516 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 453 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 390 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–F · 389 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3PML · crystal structure of a polymerase lambda variant with a dGTP analog opposite a templating… · the same entry in another collection · chain G against G, 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 0.97
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 3PML · PDBe 3PML · UniProt Q9UGP5
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