MolNFT v1 · #116676 · protein + DNA
Ternary crystal structure of polymerase lambda with a ga mispair at the primer terminus with CA2+ in the active
5DKW · DNA polymerase lambda: “Ternary crystal structure of polymerase lambda with a ga mispair at the primer terminus with CA2+ in the…”. X-ray diffraction, 2 ligands (DTP, CA), 8 pockets (best druggability 0.73). MolNFT v1 #116676 on…
- PDB
- 5DKW
- Type
- protein + DNA
- Length
- 680 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(P*GP*CP*CP*G)-3'); DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- DTP, CA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase lambda (EC 2.7.7.7) | protein | 319 | 48% helix, 15% strand | Q9UGP5 |
| D, C | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| P, E | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| T, F | DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, P, T, B, E, F
- CA · Calcium ion · metal · 5 copies · chains A, D, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.73 | 0.77 | 104 | empty |
| 2 | 1026 | 0.71 | 0.75 | 51 | DTP, CA |
| 3 | 94 | 0.70 | 0.94 | 16 | empty |
| 4 | 1121 | 0.69 | 0.74 | 58 | DTP, CA |
| 5 | 135 | 0.56 | 0.83 | 23 | empty |
Interfaces
15 interfaces between chains.
- A–T · 615 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 600 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 520 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 379 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 5DKW · Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain B 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 5DKW · PDBe 5DKW · UniProt Q9UGP5
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