Research workbench
DNA polymerase lambda in complex with a DNA duplex containing an unpaired dtmp
Analyse DNA polymerase lambda in complex with a DNA duplex containing an unpaired dtmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BCQ
- Type
- protein + DNA
- Length
- 347 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*CP*G)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- PPV, NA, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 48% 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*CP*G)-3' | dna | 7 | — | — |
| T | 5'-D(*CP*GP*GP*CP*CP*GP*TP*TP*AP*CP*TP*G)-3' | dna | 12 | — | — |
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 48% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains P, A
- NA · Sodium ion · metal · 3 copies · chains P, A, T
- MG · Magnesium ion · metal · chains P, A
- EDO · 1,2-ethanediol · additive · chains T, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.69 | 0.74 | 65 | MG, PPV |
| 2 | 123 | 0.59 | 0.85 | 30 | EDO |
| 3 | 313 | 0.53 | 0.74 | 26 | empty |
| 4 | 128 | 0.51 | 0.81 | 20 | empty |
Interfaces
5 interfaces between chains.
- T–A · 1030 Ų buried · 21 hydrogen bonds · protein-nucleic
- P–A · 582 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–A · 380 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 325 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- D–T · 189 Ų buried · 13 hydrogen bonds · nucleic-nucleic
Compared structures
- 2BCQ · DNA polymerase lambda in complex with 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 2BCQ · PDBe 2BCQ · UniProt Q9UGP5
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