MolNFT v1 · #31984 · protein + DNA
DNA polymerase lambda in complex with a DNA duplex containing an unpaired damp
2BCR · 5'-D(P*GP*CP*CP*G)-3': “DNA polymerase lambda in complex with a DNA duplex containing an unpaired damp”. X-ray diffraction, 3 ligands (PPV, NA, MG), 4 pockets (best druggability 0.69). MolNFT v1 #31984 on GenesisL1: 3D structure…
- PDB
- 2BCR
- Type
- protein + DNA
- Length
- 348 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 · 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*CP*G)-3' | dna | 7 | — | — |
| T | 5'-D(*CP*GP*GP*CP*CP*GP*AP*TP*AP*CP*TP*G)-3' | dna | 12 | — | — |
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 47% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains P, A
- NA · Sodium ion · metal · 3 copies · chains T, A, P, D
- MG · Magnesium ion · metal · chains P, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains P, A, T
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 | 991 | 0.69 | 0.74 | 58 | MG, PPV |
| 2 | 114 | 0.60 | 0.86 | 31 | EDO |
| 3 | 265 | 0.51 | 0.75 | 26 | empty |
| 4 | 125 | 0.51 | 0.81 | 22 | empty |
Interfaces
5 interfaces between chains.
- T–A · 1047 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–A · 590 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–A · 394 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 325 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- D–T · 189 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Compared structures
- 2BCR · DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp · 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 2BCR · PDBe 2BCR · UniProt Q9UGP5
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