Research workbench
Structure of a ternary complex of the R517K pol lambda mutant
Analyse Structure of a ternary complex of the R517K pol lambda mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5G
- Type
- protein + DNA
- Length
- 695 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- D3T, NA, MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 49% helix, 13% strand | Q9UGP5 |
| T, U | DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3') | dna | 11 | — | — |
| P, Q | DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3') | dna | 6 | — | — |
| D, E | DNA (5'-D(P*DGP*DCP*DCP*DG)-3') | dna | 4 | — | — |
| B | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 329 | 48% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · 2 copies · chains A, T, P, B, U, Q
- NA · Sodium ion · metal · 8 copies · chains A, P, D, B, Q, E
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains T, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.80 | 0.95 | 31 | empty |
| 2 | 1154 | 0.75 | 0.78 | 97 | empty |
| 3 | 955 | 0.73 | 0.77 | 67 | D3T, MG, NA |
| 4 | 837 | 0.72 | 0.77 | 61 | MG, D3T |
| 5 | 91 | 0.57 | 0.86 | 23 | empty |
Interfaces
15 interfaces between chains.
- A–T · 806 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–U · 751 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 654 Ų buried · 7 hydrogen bonds · protein-protein
- A–P · 394 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 381 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
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 3C5G · PDBe 3C5G · UniProt Q9UGP5
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