Research workbench
Structure of a binary complex of the R517A pol lambda mutant
Analyse Structure of a binary complex of the R517A 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
- 3C5F
- Type
- protein + DNA
- Length
- 694 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- NA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T, U | DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3') | dna | 11 | — | — |
| P, Q | DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3') | dna | 6 | — | — |
| D, E | DNA (5'-D(P*DGP*DCP*DCP*DG)-3') | dna | 4 | — | — |
| A, B | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 49% helix, 13% strand | Q9UGP5 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains D, A, P, Q, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.72 | 0.80 | 71 | NA |
| 2 | 857 | 0.70 | 0.76 | 65 | empty |
| 3 | 446 | 0.67 | 0.79 | 46 | empty |
| 4 | 151 | 0.60 | 0.84 | 21 | empty |
| 5 | 302 | 0.58 | 0.77 | 33 | empty |
Interfaces
15 interfaces between chains.
- T–A · 821 Ų buried · 12 hydrogen bonds · protein-nucleic
- U–B · 816 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–B · 564 Ų buried · 6 hydrogen bonds · protein-protein
- E–B · 391 Ų buried · 13 hydrogen bonds · protein-nucleic
- Q–B · 389 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (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 3C5F · PDBe 3C5F · UniProt Q9UGP5
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