Research workbench
DNA polymerase lambda in complex with dttp and a DNA duplex containing an unpaired dtmp
Analyse DNA polymerase lambda in complex with dttp and a DNA duplex containing an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BCV
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*GP*CP*CP*G)-3'; 5'-D(*CP*AP*GP*TP*AP*(O2C))-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- TTP, NA, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| P | 5'-D(*CP*AP*GP*TP*AP*(O2C))-3' | dna | 6 | — | — |
| T | 5'-D(*CP*GP*GP*CP*AP*GP*TP*TP*AP*CP*TP*G)-3' | dna | 12 | — | — |
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 323 | 47% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains P, T, A
- NA · Sodium ion · metal · 3 copies · chains P, A, T
- MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.68 | 0.75 | 58 | MG, NA, TTP |
| 2 | 133 | 0.51 | 0.80 | 22 | empty |
| 3 | 265 | 0.48 | 0.74 | 24 | empty |
| 4 | 65 | 0.35 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- T–A · 1029 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–A · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 374 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 287 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- D–T · 191 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2BCV · DNA polymerase lambda in complex with Dttp and a DNA duplex containing an unpaired Dtmp · 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 2BCV · PDBe 2BCV · UniProt Q9UGP5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.