MolNFT v1 · #116449 · protein
Binary complex of human polymerase lambda with dctp
5DDY · DNA polymerase lambda: “Binary complex of human polymerase lambda with dctp”. X-ray diffraction, 3 ligands (DCP, MN, MG), 9 pockets (best druggability 0.82). MolNFT v1 #116449 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DDY
- Type
- protein
- Length
- 1,142 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- DCP, MN, MG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA polymerase lambda (EC 2.7.7.7) | protein | 327 | 44% helix, 17% strand | Q9UGP5 |
| E, G | DNA polymerase lambda (EC 2.7.7.7) | protein | 244 | 40% helix, 17% strand | Q9UGP5 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- MN · Manganese (II) ion · metal · 8 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.82 | 0.85 | 68 | empty |
| 2 | 385 | 0.67 | 0.80 | 41 | empty |
| 3 | 394 | 0.61 | 0.77 | 41 | MN, DCP |
| 4 | 85 | 0.60 | 0.88 | 21 | empty |
| 5 | 108 | 0.51 | 0.83 | 28 | MN |
Interfaces
3 interfaces between chains.
- A–C · 837 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 555 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 185 Ų buried · 0 hydrogen bonds · protein-protein
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 5DDY · PDBe 5DDY · UniProt Q9UGP5
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