MolNFT v1 · #66655 · protein + DNA
Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched da
3HWT: “Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched da”. X-ray diffraction, 3 ligands (D3T, MG, NA), 4 pockets (best druggability 0.67). MolNFT v1 #66655 on GenesisL1: 3D…
- PDB
- 3HWT
- Type
- protein + DNA
- Length
- 341 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- D3T, MG, NA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 319 | 48% helix, 14% strand | Q9UGP5 |
| T | 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3' | dna | 12 | — | — |
| P | 5'-D(*CP*AP*GP*TP*AP*(2DT))-3' | dna | 6 | — | — |
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A, P
- EDO · 1,2-ethanediol · additive · 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 | 781 | 0.67 | 0.75 | 53 | D3T, MG, NA |
| 2 | 77 | 0.52 | 0.85 | 26 | empty |
| 3 | 93 | 0.41 | 0.78 | 16 | empty |
| 4 | 105 | 0.41 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–T · 1095 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 378 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 374 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–P · 285 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- T–D · 187 Ų buried · 13 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3HWT · Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate… · the same entry in another collection · chain A against A, 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 0.97
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 3HWT · PDBe 3HWT · UniProt Q9UGP5
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