Research workbench
Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating a and an incoming 8-oxo-dgtp
Analyse Crystal structure of the pre-catalytic ternary 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
- 4XA5
- Type
- protein + DNA
- Length
- 335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; Downstream primer DNA (5'-D(P*GP*CP*CP*G)-3'); Primer DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- 8DG, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 314 | 50% helix, 13% strand | Q9UGP5 |
| D | Downstream primer DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| P | Primer DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3') | dna | 6 | — | — |
| T | Template DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, P
- ACT · Acetate ion · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.67 | 0.74 | 50 | 8DG, MG |
| 2 | 107 | 0.59 | 0.86 | 27 | ACT, GOL |
| 3 | 298 | 0.55 | 0.76 | 25 | empty |
| 4 | 102 | 0.53 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–T · 837 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 386 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 377 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 283 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- D–T · 192 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (artifact, nucleotide modification).
Compared structures
- 4XA5 · Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a… · the same entry in another collection · chain D against D, 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 4XA5 · PDBe 4XA5 · UniProt Q9UGP5
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